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Sample records for allen brain atlas

  1. Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

    PubMed

    Kuan, Leonard; Li, Yang; Lau, Chris; Feng, David; Bernard, Amy; Sunkin, Susan M; Zeng, Hongkui; Dang, Chinh; Hawrylycz, Michael; Ng, Lydia

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

  2. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

    PubMed Central

    Sunkin, Susan M.; Ng, Lydia; Lau, Chris; Dolbeare, Tim; Gilbert, Terri L.; Thompson, Carol L.; Hawrylycz, Michael; Dang, Chinh

    2013-01-01

    The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal. PMID:23193282

  3. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.

    PubMed

    Sunkin, Susan M; Ng, Lydia; Lau, Chris; Dolbeare, Tim; Gilbert, Terri L; Thompson, Carol L; Hawrylycz, Michael; Dang, Chinh

    2013-01-01

    The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.

  4. Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.

    PubMed

    Zaldivar, Andrew; Krichmar, Jeffrey L

    2014-01-01

    The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources.

  5. Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome

    NASA Astrophysics Data System (ADS)

    Abdelmoula, Walid M.; Carreira, Ricardo J.; Shyti, Reinald; Balluff, Benjamin; Tolner, Else; van den Maagdenberg, Arn M. J. M.; Lelieveldt, B. P. F.; McDonnell, Liam; Dijkstra, Jouke

    2014-03-01

    Imaging Mass Spectrometry (IMS) is an emerging molecular imaging technology that provides spatially resolved information on biomolecular structures; each image pixel effectively represents a molecular mass spectrum. By combining the histological images and IMS-images, neuroanatomical structures can be distinguished based on their biomolecular features as opposed to morphological features. The combination of IMS data with spatially resolved gene expression maps of the mouse brain, as provided by the Allen Mouse Brain atlas, would enable comparative studies of spatial metabolic and gene expression patterns in life-sciences research and biomarker discovery. As such, it would be highly desirable to spatially register IMS slices to the Allen Brain Atlas (ABA). In this paper, we propose a multi-step automatic registration pipeline to register ABA histology to IMS- images. Key novelty of the method is the selection of the best reference section from the ABA, based on pre-processed histology sections. First, we extracted a hippocampus-specific geometrical feature from the given experimental histological section to initially localize it among the ABA sections. Then, feature-based linear registration is applied to the initially localized section and its two neighbors in the ABA to select the most similar reference section. A non-rigid registration yields a one-to-one mapping of the experimental IMS slice to the ABA. The pipeline was applied on 6 coronal sections from two mouse brains, showing high anatomical correspondence, demonstrating the feasibility of complementing biomolecule distributions from individual mice with the genome-wide ABA transcriptome.

  6. A Self-Study Tutorial using the Allen Brain Explorer and Brain Atlas to Teach Concepts of Mammalian Neuroanatomy and Brain Function.

    PubMed

    Jenks, Bruce G

    2009-01-01

    The Allen Brain Atlas is a repository of neuroanatomical data concerning the mouse brain. The core of the database is a Nissl-stained reference atlas of the brain accompanied by in situ hybridization data for essentially the entire mouse genome. This database is freely available at the Allen Institute for Brain Science website, as is an innovative tool to explore the database, the Brain Explorer. This tool is downloaded and installed on your own computer. I have developed a self-study tutorial, "Explorations with the Allen Brain Explorer", which uses the Brain Explorer and the Brain Atlas to teach fundamentals of mammalian neuroanatomy and brain function. In this tutorial background information and step-by-step exercises on the use of the Brain Explorer are given using PowerPoint as a platform. To do the tutorial both the PowerPoint and the Brain Explorer are opened on the computer and the students switch from one program to the other as they go, in a step-wise fashion, through the various exercises. There are two main groups of exercises, titled "The Basics" and "Explorations", with both groups accessed from a PowerPoint "Start Menu" by clicking on dynamic links to the appropriate exercises. Most exercises have a number of dynamic links to PowerPoint slides where background information for the exercises is given or the neuroanatomical data collected from the Brain Atlas is discussed.

  7. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  8. Patterned expression of ion channel genes in mouse dorsal raphe nucleus determined with the Allen Mouse Brain Atlas

    PubMed Central

    Templin, J. Scott; Bang, Sun Jung; Soiza-Reilly, Mariano; Berde, Charles B.; Commons, Kathryn G.

    2012-01-01

    The dorsal raphe nucleus (DR) is the major source of serotonin (5-hydroxytryptamine, 5-HT) in the forebrain and dysfunction of this midbrain structure is implicated in affective disorders. The DR is composed of several types of 5-HT and non-5-HT neurons and their excitable-membrane properties are heterogeneous and overlapping. In order to understand how these properties may be generated, we examined the mRNA expression patterns of voltage- and ligand-gated ion channels in the DR using the Allen Mouse Brain Atlas. Since DR cytoarchitecture is organized with respect to the midline, we sought to identify genes that were expressed in a pattern with respect to the midline, either enriched or depleted, rather than those that were homogenously expressed throughout the DR. Less than 10% of the screened genes for voltage-gated ion channels showed patterned expression within the DR. Identified genes included voltage-gated sodium channel beta subunits, potassium channels, P/Q-, N-type calcium channels, as well as the alpha2/delta-1 calcium channel. Several voltage-gated chloride channels were also identified, although these may function within intracellular compartments. Of the ligand-gated ion channels examined, 20% showed patterned expression. These consisted primarily of glutamate and GABA-A receptor subunits. The identified genes likely contribute to unique excitable properties of different groups of neurons in the DR and may include novel pharmacologic targets for affective disorders. PMID:22534482

  9. Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

    PubMed

    Eising, Else; Huisman, Sjoerd M H; Mahfouz, Ahmed; Vijfhuizen, Lisanne S; Anttila, Verneri; Winsvold, Bendik S; Kurth, Tobias; Ikram, M Arfan; Freilinger, Tobias; Kaprio, Jaakko; Boomsma, Dorret I; van Duijn, Cornelia M; Järvelin, Marjo-Riitta R; Zwart, John-Anker; Quaye, Lydia; Strachan, David P; Kubisch, Christian; Dichgans, Martin; Davey Smith, George; Stefansson, Kari; Palotie, Aarno; Chasman, Daniel I; Ferrari, Michel D; Terwindt, Gisela M; de Vries, Boukje; Nyholt, Dale R; Lelieveldt, Boudewijn P F; van den Maagdenberg, Arn M J M; Reinders, Marcel J T

    2016-04-01

    Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology.

  10. MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas

    PubMed Central

    Rizzo, Gaia; Veronese, Mattia; Expert, Paul; Turkheimer, Federico E.; Bertoldo, Alessandra

    2016-01-01

    Introduction Brain-wide mRNA mappings offer a great potential for neuroscience research as they can provide information about system proteomics. In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. This approach is potentially applicable to any imaging modality as long as an efficient procedure of imaging-genomic matching is provided. In the original work we considered mRNA brain maps of the whole human genome derived from the Allen human brain database (ABA) and we performed the analysis with a specific region-based segmentation with a resolution that was limited by the PET data parcellation. There we identified the need for a platform for imaging-genomic integration that should be usable with any imaging modalities and fully exploit the high resolution mapping of ABA dataset. Aim In this work we present MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis), a software platform that allows the investigation of the correlation patterns between neuroimaging data of any sort (both functional and structural) with mRNA gene expression profiles derived from the ABA database at high resolution. Results We applied MENGA to six different imaging datasets from three modalities (PET, single photon emission tomography and magnetic resonance imaging) targeting the dopamine and serotonin receptor systems and the myelin molecular structure. We further investigated imaging-genomic correlations in the case of mismatch between selected proteins and imaging targets. PMID:26882227

  11. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  12. Comprehensive cellular‐resolution atlas of the adult human brain

    PubMed Central

    Royall, Joshua J.; Sunkin, Susan M.; Ng, Lydia; Facer, Benjamin A.C.; Lesnar, Phil; Guillozet‐Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A.; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A.; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L.; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A.; Koch, Christof; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Zielke, H. Ronald; Hohmann, John G.; Jones, Allan R.; Bernard, Amy; Hawrylycz, Michael J.; Hof, Patrick R.; Fischl, Bruce

    2016-01-01

    ABSTRACT Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

  13. Computerized Anatomy Atlas Of The Human Brain

    NASA Astrophysics Data System (ADS)

    Adair, Taylor; Bajcsy, Ruzena; Karp, Peter; Stein, Alan

    1981-10-01

    A software for developing, editing and displaying a 3-D computerized anatomic atlas of a human brain is described. The objective of this atlas is to serve as a reference in identifying various structures in CT scans.

  14. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

    PubMed Central

    Zaslavsky, Ilya; Baldock, Richard A.; Boline, Jyl

    2014-01-01

    Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project. PMID

  15. Multiple brain atlas database and atlas-based neuroimaging system.

    PubMed

    Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

    1997-01-01

    For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

  16. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.

    PubMed

    Thompson, Carol L; Ng, Lydia; Menon, Vilas; Martinez, Salvador; Lee, Chang-Kyu; Glattfelder, Katie; Sunkin, Susan M; Henry, Alex; Lau, Christopher; Dang, Chinh; Garcia-Lopez, Raquel; Martinez-Ferre, Almudena; Pombero, Ana; Rubenstein, John L R; Wakeman, Wayne B; Hohmann, John; Dee, Nick; Sodt, Andrew J; Young, Rob; Smith, Kimberly; Nguyen, Thuc-Nghi; Kidney, Jolene; Kuan, Leonard; Jeromin, Andreas; Kaykas, Ajamete; Miller, Jeremy; Page, Damon; Orta, Geri; Bernard, Amy; Riley, Zackery; Smith, Simon; Wohnoutka, Paul; Hawrylycz, Michael J; Puelles, Luis; Jones, Allan R

    2014-07-16

    To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

  17. Towards multimodal atlases of the human brain

    PubMed Central

    Toga, Arthur W.; Thompson, Paul M.; Mori, Susumu; Amunts, Katrin; Zilles, Karl

    2010-01-01

    Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease. PMID:17115077

  18. Anatomical brain atlas for NIRS measurements of brain activation

    NASA Astrophysics Data System (ADS)

    Caffini, Matteo; Zucchelli, Lucia; Contini, Davide; Cubeddu, Rinaldo; Spinelli, Lorenzo; Boas, David; Torricelli, Alessandro

    2011-07-01

    Anatomical brain atlases have been introduced in the analysis NIRS data of brain activation and good spatial activation localization has been proved. We applied this method to visualize NIRS data from different protocols.

  19. A high-resolution in vivo atlas of the human brain's serotonin system.

    PubMed

    Beliveau, Vincent; Ganz, Melanie; Feng, Ling; Ozenne, Brice; Højgaard, Liselotte; Fisher, Patrick M; Svarer, Claus; Greve, Douglas N; Knudsen, Gitte M

    2016-11-17

    The serotonin (5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. We here present a high-resolution multi-dimensional in vivo atlas of four of the human brain's 5-HT receptors (5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4) as well as of the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) scans, acquired in a total of 210 healthy individuals. Comparison of the regional PET binding measures with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (pmol/ml). We also assessed the regional association between protein concentration and mRNA expression in the human brain by comparing the 5-HT density across the atlas to data from the Allen Human Brain atlas and identified receptor- and transporter specific associations which inform about the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system of the human brain.

  20. A High-Resolution In Vivo Atlas of the Human Brain's Serotonin System.

    PubMed

    Beliveau, Vincent; Ganz, Melanie; Feng, Ling; Ozenne, Brice; Højgaard, Liselotte; Fisher, Patrick M; Svarer, Claus; Greve, Douglas N; Knudsen, Gitte M

    2017-01-04

    The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4) and the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of positron emission tomography (PET) and magnetic resonance imaging (MRI) scans acquired in a total of 210 healthy individuals. Comparison of the regional PET binding measures with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (in picomoles per milliliter). We also assessed the regional association between protein concentration and mRNA expression in the human brain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific associations that show the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system of the human brain.

  1. Probabilistic brain atlas encoding using Bayesian inference.

    PubMed

    Van Leemput, Koen

    2006-01-01

    This paper addresses the problem of creating probabilistic brain atlases from manually labeled training data. We propose a general mesh-based atlas representation, and compare different atlas models by evaluating their posterior probabilities and the posterior probabilities of their parameters. Using such a Baysian framework, we show that the widely used "average" brain atlases constitute relatively poor priors, partly because they tend to overfit the training data, and partly because they do not allow to align corresponding anatomical features across datasets. We also demonstrate that much more powerful representations can be built using content-adaptive meshes that incorporate non-rigid deformation field models. We believe extracting optimal prior probability distributions from training data is crucial in light of the central role priors play in many automated brain MRI analysis techniques.

  2. A digital atlas of the dog brain.

    PubMed

    Datta, Ritobrato; Lee, Jongho; Duda, Jeffrey; Avants, Brian B; Vite, Charles H; Tseng, Ben; Gee, James C; Aguirre, Gustavo D; Aguirre, Geoffrey K

    2012-01-01

    There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI) studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1) A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head); 2) A co-registered, high-resolution (0.33 mm isotropic) template created from imaging of ex-vivo brains at 7 Tesla; 3) A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features). The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta).

  3. A Digital Atlas of the Dog Brain

    PubMed Central

    Datta, Ritobrato; Lee, Jongho; Duda, Jeffrey; Avants, Brian B.; Vite, Charles H.; Tseng, Ben; Gee, James C.; Aguirre, Gustavo D.; Aguirre, Geoffrey K.

    2012-01-01

    There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI) studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1) A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head); 2) A co-registered, high-resolution (0.33 mm isotropic) template created from imaging of ex-vivo brains at 7 Tesla; 3) A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features). The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta). PMID:23284904

  4. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM

    NASA Astrophysics Data System (ADS)

    Kutten, Kwame S.; Vogelstein, Joshua T.; Charon, Nicolas; Ye, Li; Deisseroth, Karl; Miller, Michael I.

    2016-04-01

    The CLARITY method renders brains optically transparent to enable high-resolution imaging in the structurally intact brain. Anatomically annotating CLARITY brains is necessary for discovering which regions contain signals of interest. Manually annotating whole-brain, terabyte CLARITY images is difficult, time-consuming, subjective, and error-prone. Automatically registering CLARITY images to a pre-annotated brain atlas offers a solution, but is difficult for several reasons. Removal of the brain from the skull and subsequent storage and processing cause variable non-rigid deformations, thus compounding inter-subject anatomical variability. Additionally, the signal in CLARITY images arises from various biochemical contrast agents which only sparsely label brain structures. This sparse labeling challenges the most commonly used registration algorithms that need to match image histogram statistics to the more densely labeled histological brain atlases. The standard method is a multiscale Mutual Information B-spline algorithm that dynamically generates an average template as an intermediate registration target. We determined that this method performs poorly when registering CLARITY brains to the Allen Institute's Mouse Reference Atlas (ARA), because the image histogram statistics are poorly matched. Therefore, we developed a method (Mask-LDDMM) for registering CLARITY images, that automatically finds the brain boundary and learns the optimal deformation between the brain and atlas masks. Using Mask-LDDMM without an average template provided better results than the standard approach when registering CLARITY brains to the ARA. The LDDMM pipelines developed here provide a fast automated way to anatomically annotate CLARITY images; our code is available as open source software at http://NeuroData.io.

  5. The cerefy brain atlases: continuous enhancement of the electronic talairach-tournoux brain atlas.

    PubMed

    Nowinski, Wieslaw L

    2005-01-01

    The Talairach-Tournoux (TT) atlas is probably the most often used brain atlas. We overview briefly the activities in developments of electronic versions of the TT atlas and focus on our more than 10-yr efforts in its continuous enhancement resulting in three main versions: TT-1997, TT-2000, and TT-2004. The recent TT-2004 version is substantially improved over the digitized print original with a higher structure parcellation, better quality and resolution of individual structures, and improved three-dimensional (3D) spatial consistency. It is also much more suitable for developing atlas-based applications owing to pure color-coding (for automatic structure labeling), contour representation (to avoid scan blocking by the overlaid atlas), and color cross-atlas consistency (for the simultaneous use of multiple atlases). We also provide a procedure for 3D spatial consistency improvement and illustrate its use. Finally, we present some of our latest atlas-assisted applications for fast and automatic interpretation of morphological, stroke, and molecular images, and discuss the future steps in TT atlas enhancement.

  6. Interoperable atlases of the human brain.

    PubMed

    Amunts, K; Hawrylycz, M J; Van Essen, D C; Van Horn, J D; Harel, N; Poline, J-B; De Martino, F; Bjaalie, J G; Dehaene-Lambertz, G; Dehaene, S; Valdes-Sosa, P; Thirion, B; Zilles, K; Hill, S L; Abrams, M B; Tass, P A; Vanduffel, W; Evans, A C; Eickhoff, S B

    2014-10-01

    The last two decades have seen an unprecedented development of human brain mapping approaches at various spatial and temporal scales. Together, these have provided a large fundus of information on many different aspects of the human brain including micro- and macrostructural segregation, regional specialization of function, connectivity, and temporal dynamics. Atlases are central in order to integrate such diverse information in a topographically meaningful way. It is noteworthy, that the brain mapping field has been developed along several major lines such as structure vs. function, postmortem vs. in vivo, individual features of the brain vs. population-based aspects, or slow vs. fast dynamics. In order to understand human brain organization, however, it seems inevitable that these different lines are integrated and combined into a multimodal human brain model. To this aim, we held a workshop to determine the constraints of a multi-modal human brain model that are needed to enable (i) an integration of different spatial and temporal scales and data modalities into a common reference system, and (ii) efficient data exchange and analysis. As detailed in this report, to arrive at fully interoperable atlases of the human brain will still require much work at the frontiers of data acquisition, analysis, and representation. Among them, the latter may provide the most challenging task, in particular when it comes to representing features of vastly different scales of space, time and abstraction. The potential benefits of such endeavor, however, clearly outweigh the problems, as only such kind of multi-modal human brain atlas may provide a starting point from which the complex relationships between structure, function, and connectivity may be explored.

  7. Practical MRI atlas of neonatal brain development

    SciTech Connect

    Barkovich, A.J.; Truwit, C.L.

    1990-01-01

    This book is an anatomical reference for cranial magnetic resonance imaging (MRI) studies in neonates and infants. It contains 122 clear, sharp MRI scans and drawings showing changes in the normal appearance of the brain and skull during development. Sections of the atlas depict the major processes of maturation: brain myelination, development of the corpus callosum, development of the cranial bone marrow, and iron deposition in the brain. High-quality scans illustrate how these changes appear on magnetic resonance images during various stages of development.

  8. Schaltenbrand-Wahren-Talairach-Tournoux brain atlas registration

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Fang, Anthony; Nguyen, Bonnie T.

    1995-04-01

    The CIeMed electronic brain atlas system contains electronic versions of multiple paper brain atlases with 3D extensions; some other 3D brain atlases are under development. Its primary goal is to provide automatic labeling and quantification of brains. The atlas data are digitized, enhanced, color coded, labeled, and organized into volumes. The atlas system provides several tools for registration, 3D display and real-time manipulation, object extraction/editing, quantification, image processing and analysis, reformatting, anatomical index operations, and file handling. The two main stereotactic atlases provided by the system are electronic and enhanced versions of Atlas of Stereotaxy of the Human Brain by Schaltenbrand and Wahren and Co-Planar Stereotactic Atlas of the Human Brain by Talairach and Tournoux. Each of these atlases has its own strengths and their combination has several advantages. First, a complementary information is merged and provided to the user. Second, the user can register data with a single atlas only, as the Schaltenbrand-Wahren-Talairach-Tournoux registration is data-independent. And last but not least, a direct registration of the Schaltenbrand-Wahren microseries with MRI data may not be feasible, since cerebral deep structures are usually not clearly discernible on MRI images. This paper addresses registration of the Schaltenbrand- Wahren and Talairach-Tournoux brain atlases. A modified proportional grid system transformation is introduced and suitable sets of landmarks identifiable in both atlases are defined. The accuracy of registration is discussed. A continuous navigation in the multi- atlas/patient data space is presented.

  9. A fast atlas pre-selection procedure for multi-atlas based brain segmentation.

    PubMed

    Ma, Jingbo; Ma, Heather T; Li, Hengtong; Ye, Chenfei; Wu, Dan; Tang, Xiaoying; Miller, Michael; Mori, Susumu

    2015-01-01

    Multi-atlas based MR image segmentation has been recognized as a quantitative analysis approach for brain. For such purpose, atlas databases keep increasing to include various anatomical characteristics of human brain. Atlas pre-selection becomes a necessary step for efficient and accurate automated segmentation of human brain images. In this study, we proposed a method of atlas pre-selection for target image segmentation on the MriCloud platform, which is a state-of-the-art multi-atlas based segmentation tool. In the MRIcloud pipeline, segmentation of lateral ventricle (LV) label is generated as an additional input in the segmentation pipeline. Under this circumstance, similarity of the LV label between target image and atlases was adopted as the atlas ranking scheme. Dice overlap coefficient was calculated and taken as the quantitative measure for atlas ranking. Segmentation results based on the proposed method were compared with that based on atlas pre-selection by mutual information (MI) between images. The final segmentation results showed a comparable accuracy of the proposed method with that from MI based atlas pre-selection. However, the computation load for the atlas pre-selection was speeded up by about 20 times compared to MI based pre-selection. The proposed method provides a promising assistance for quantitative analysis of brain images.

  10. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  11. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  12. Integrative analysis of the connectivity and gene expression atlases in the mouse brain.

    PubMed

    Ji, Shuiwang; Fakhry, Ahmed; Deng, Houtao

    2014-01-01

    Brain function is the result of interneuron signal transmission controlled by the fundamental biochemistry of each neuron. The biochemical content of a neuron is in turn determined by spatiotemporal gene expression and regulation encoded into the genomic regulatory networks. It is thus of particular interest to elucidate the relationship between gene expression patterns and connectivity in the brain. However, systematic studies of this relationship in a single mammalian brain are lacking to date. Here, we investigate this relationship in the mouse brain using the Allen Brain Atlas data. We employ computational models for predicting brain connectivity from gene expression data. In addition to giving competitive predictive performance, these models can rank the genes according to their predictive power. We show that gene expression is predictive of connectivity in the mouse brain when the connectivity signals are discretized. When the expression patterns of 4084 genes are used, we obtain a predictive accuracy of 93%. Our results also show that a small number of genes can almost give the full predictive power of using thousands of genes. We can achieve a prediction accuracy of 91% by using only 25 genes. Gene ontology analysis of the highly ranked genes shows that they are enriched for connectivity related processes.

  13. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states.

  14. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture

    PubMed Central

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.; Yu, Chunshui; Jiang, Tianzi

    2016-01-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  15. The SRI24 multichannel brain atlas: construction and applications

    NASA Astrophysics Data System (ADS)

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2008-03-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T I-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain.

  16. Multi-atlas based segmentation of brain images: atlas selection and its effect on accuracy.

    PubMed

    Aljabar, P; Heckemann, R A; Hammers, A; Hajnal, J V; Rueckert, D

    2009-07-01

    Quantitative research in neuroimaging often relies on anatomical segmentation of human brain MR images. Recent multi-atlas based approaches provide highly accurate structural segmentations of the brain by propagating manual delineations from multiple atlases in a database to a query subject and combining them. The atlas databases which can be used for these purposes are growing steadily. We present a framework to address the consequent problems of scale in multi-atlas segmentation. We show that selecting a custom subset of atlases for each query subject provides more accurate subcortical segmentations than those given by non-selective combination of random atlas subsets. Using a database of 275 atlases, we tested an image-based similarity criterion as well as a demographic criterion (age) in a leave-one-out cross-validation study. Using a custom ranking of the database for each subject, we combined a varying number n of atlases from the top of the ranked list. The resulting segmentations were compared with manual reference segmentations using Dice overlap. Image-based selection provided better segmentations than random subsets (mean Dice overlap 0.854 vs. 0.811 for the estimated optimal subset size, n=20). Age-based selection resulted in a similar marked improvement. We conclude that selecting atlases from large databases for atlas-based brain image segmentation improves the accuracy of the segmentations achieved. We show that image similarity is a suitable selection criterion and give results based on selecting atlases by age that demonstrate the value of meta-information for selection.

  17. Towards an Elastographic Atlas of Brain Anatomy

    PubMed Central

    Guo, Jing; Hirsch, Sebastian; Fehlner, Andreas; Papazoglou, Sebastian; Scheel, Michael; Braun, Juergen; Sack, Ingolf

    2013-01-01

    Cerebral viscoelastic constants can be measured in a noninvasive, image-based way by magnetic resonance elastography (MRE) for the detection of neurological disorders. However, MRE brain maps of viscoelastic constants are still limited by low spatial resolution. Here we introduce three-dimensional multifrequency MRE of the brain combined with a novel reconstruction algorithm based on a model-free multifrequency inversion for calculating spatially resolved viscoelastic parameter maps of the human brain corresponding to the dynamic range of shear oscillations between 30 and 60 Hz. Maps of two viscoelastic parameters, the magnitude and the phase angle of the complex shear modulus, |G*| and φ, were obtained and normalized to group templates of 23 healthy volunteers in the age range of 22 to 72 years. This atlas of the anatomy of brain mechanics reveals a significant contrast in the stiffness parameter |G*| between different anatomical regions such as white matter (WM; 1.252±0.260 kPa), the corpus callosum genu (CCG; 1.104±0.280 kPa), the thalamus (TH; 1.058±0.208 kPa) and the head of the caudate nucleus (HCN; 0.649±0.101 kPa). φ, which is sensitive to the lossy behavior of the tissue, was in the order of CCG (1.011±0.172), TH (1.037±0.173), CN (0.906±0.257) and WM (0.854±0.169). The proposed method provides the first normalized maps of brain viscoelasticity with anatomical details in subcortical regions and provides useful background data for clinical applications of cerebral MRE. PMID:23977148

  18. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

  19. Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

    PubMed

    Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

    2016-01-15

    Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation.

  20. Whole-brain activity mapping onto a zebrafish brain atlas.

    PubMed

    Randlett, Owen; Wee, Caroline L; Naumann, Eva A; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E; Portugues, Ruben; Lacoste, Alix M B; Riegler, Clemens; Engert, Florian; Schier, Alexander F

    2015-11-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.

  1. UNC-Emory Infant Atlases for Macaque Brain Image Analysis: Postnatal Brain Development through 12 Months

    PubMed Central

    Shi, Yundi; Budin, Francois; Yapuncich, Eva; Rumple, Ashley; Young, Jeffrey T.; Payne, Christa; Zhang, Xiaodong; Hu, Xiaoping; Godfrey, Jodi; Howell, Brittany; Sanchez, Mar M.; Styner, Martin A.

    2017-01-01

    Computational anatomical atlases have shown to be of immense value in neuroimaging as they provide age appropriate reference spaces alongside ancillary anatomical information for automated analysis such as subcortical structural definitions, cortical parcellations or white fiber tract regions. Standard workflows in neuroimaging necessitate such atlases to be appropriately selected for the subject population of interest. This is especially of importance in early postnatal brain development, where rapid changes in brain shape and appearance render neuroimaging workflows sensitive to the appropriate atlas choice. We present here a set of novel computation atlases for structural MRI and Diffusion Tensor Imaging as crucial resource for the analysis of MRI data from non-human primate rhesus monkey (Macaca mulatta) data in early postnatal brain development. Forty socially-housed infant macaques were scanned longitudinally at ages 2 weeks, 3, 6, and 12 months in order to create cross-sectional structural and DTI atlases via unbiased atlas building at each of these ages. Probabilistic spatial prior definitions for the major tissue classes were trained on each atlas with expert manual segmentations. In this article we present the development and use of these atlases with publicly available tools, as well as the atlases themselves, which are publicly disseminated to the scientific community. PMID:28119564

  2. Waxholm Space atlas of the Sprague Dawley rat brain.

    PubMed

    Papp, Eszter A; Leergaard, Trygve B; Calabrese, Evan; Johnson, G Allan; Bjaalie, Jan G

    2014-08-15

    Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces.

  3. Combining Multi-atlas Segmentation with Brain Surface Estimation.

    PubMed

    Huo, Yuankai; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-02-27

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitations in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

  4. Combining multi-atlas segmentation with brain surface estimation

    NASA Astrophysics Data System (ADS)

    Huo, Yuankai; Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-03-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

  5. Combining Multi-atlas Segmentation with Brain Surface Estimation

    PubMed Central

    Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-01-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this “segmentation to surface to parcellation” strategy has shown limitations in various situations. In this work, we propose a novel “multi-atlas segmentation to surface” method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly

  6. A new neonatal cortical and subcortical brain atlas: the Melbourne Children's Regional Infant Brain (M-CRIB) atlas.

    PubMed

    Alexander, Bonnie; Murray, Andrea L; Loh, Wai Yen; Matthews, Lillian G; Adamson, Chris; Beare, Richard; Chen, Jian; Kelly, Claire E; Rees, Sandra; Warfield, Simon K; Anderson, Peter J; Doyle, Lex W; Spittle, Alicia J; Cheong, Jeanie L Y; Seal, Marc L; Thompson, Deanne K

    2017-02-15

    Investigating neonatal brain structure and function can offer valuable insights into behaviour and cognition in healthy and clinical populations; both at term age, and longitudinally in comparison with later time points. Parcellated brain atlases for adult populations are readily available, however warping infant data to adult template space is not ideal due to morphological and tissue differences between these groups. Several parcellated neonatal atlases have been developed, although there remains strong demand for manually parcellated ground truth data with detailed cortical definition. Additionally, compatibility with existing adult atlases is favourable for use in longitudinal investigations. We aimed to address these needs by replicating the widely-used Desikan-Killiany (2006) adult cortical atlas in neonates. We also aimed to extend brain coverage by complementing this cortical scheme with basal ganglia, thalamus, cerebellum and other subcortical segmentations. Thus, we have manually parcellated these areas volumetrically using high-resolution neonatal T2-weighted MRI scans, and initial automated and manually edited tissue classification, providing 100 regions in all. Linear and nonlinear T2-weighted structural templates were also generated. In this paper we provide manual parcellation protocols, and present the parcellated probability maps and structural templates together as the Melbourne Children's Regional Infant Brain (M-CRIB) atlas.

  7. Atlas-guided segmentation of vervet monkey brain MRI.

    PubMed

    Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

    2011-01-01

    The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model.

  8. Atlas-Guided Segmentation of Vervet Monkey Brain MRI

    PubMed Central

    Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

    2011-01-01

    The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model. PMID:22253661

  9. Stereotactic PET atlas of the human brain: Aid for visual interpretation of functional brain images

    SciTech Connect

    Minoshima, S.; Koeppe, R.A.; Frey, A.; Ishihara, M.; Kuhl, D.E.

    1994-06-01

    In the routine analysis of functional brain images obtained by PET, subjective visual interpretation is often used for anatomic localization. To enhance the accuracy and consistency of the anatomic interpretation, a PET stereotactic atlas and localization approach was designed for functional brain images. The PET atlas was constructed from a high-resolution [{sup 18}F]fluorodeoxyglucose (FDG) image set of a normal volunteer (a 41-yr-ld woman). The image set was reoriented stereotactically, according to the intercommissural (anterior and posterior commissures) line and transformed to the standard stereotactic atlas coordinates. Cerebral structures were annotated on the transaxial planes using a proportional grid system and surface-rendered images. The stereotactic localization technique was applied to image sets from patients with Alzheimer`s disease, and areas of functional alteration were localized visually by referring to the PET atlas. Major brain structures were identified on both transaxial planes and surface-rendered images. In the stereotactic system, anatomic correspondence between the PET atlas and stereotactically reoriented individual image sets of patients with Alzheimer`s disease facilitated both indirect and direct localization of the cerebral structures. Because rapid stereotactic alignment methods for PET images are now available for routine use, the PET atlas will serve as an aid for visual interpretation of functional brain images in the stereotactic system. Widespread application of stereotactic localization may be used in functional brain images, not only in the research setting, but also in routine clinical situations. 41 refs., 3 figs.

  10. Automated 3-Dimensional Brain Atlas Fitting to Microelectrode Recordings from Deep Brain Stimulation Surgeries

    PubMed Central

    Luján, J. Luis; Noecker, Angela M.; Butson, Christopher R.; Cooper, Scott E.; Walter, Benjamin L.; Vitek, Jerrold L.; McIntyre, Cameron C.

    2009-01-01

    Objective Deep brain stimulation (DBS) surgeries commonly rely on brain atlases and microelectrode recordings (MER) to help identify the target location for electrode implantation. We present an automated method for optimally fitting a 3-dimensional brain atlas to intraoperative MER and predicting a target DBS electrode location in stereotactic coordinates for the patient. Methods We retrospectively fit a 3-dimensional brain atlas to MER points from 10 DBS surgeries targeting the subthalamic nucleus (STN). We used a constrained optimization algorithm to maximize the MER points correctly fitted (i.e., contained) within the appropriate atlas nuclei. We compared our optimization approach to conventional anterior commissure-posterior commissure (AC/PC) scaling, and to manual fits performed by four experts. A theoretical DBS electrode target location in the dorsal STN was customized to each patient as part of the fitting process and compared to the location of the clinically defined therapeutic stimulation contact. Results The human expert and computer optimization fits achieved significantly better fits than the AC/PC scaling (80, 81, and 41% of correctly fitted MER, respectively). However, the optimization fits were performed in less time than the expert fits and converged to a single solution for each patient, eliminating interexpert variance. Conclusions and Significance DBS therapeutic outcomes are directly related to electrode implantation accuracy. Our automated fitting techniques may aid in the surgical decision-making process by optimally integrating brain atlas and intraoperative neurophysiological data to provide a visual guide for target identification. PMID:19556832

  11. Whole Brain Magnetic Resonance Image Atlases: A Systematic Review of Existing Atlases and Caveats for Use in Population Imaging

    PubMed Central

    Dickie, David Alexander; Shenkin, Susan D.; Anblagan, Devasuda; Lee, Juyoung; Blesa Cabez, Manuel; Rodriguez, David; Boardman, James P.; Waldman, Adam; Job, Dominic E.; Wardlaw, Joanna M.

    2017-01-01

    Brain MRI atlases may be used to characterize brain structural changes across the life course. Atlases have important applications in research, e.g., as registration and segmentation targets to underpin image analysis in population imaging studies, and potentially in future in clinical practice, e.g., as templates for identifying brain structural changes out with normal limits, and increasingly for use in surgical planning. However, there are several caveats and limitations which must be considered before successfully applying brain MRI atlases to research and clinical problems. For example, the influential Talairach and Tournoux atlas was derived from a single fixed cadaveric brain from an elderly female with limited clinical information, yet is the basis of many modern atlases and is often used to report locations of functional activation. We systematically review currently available whole brain structural MRI atlases with particular reference to the implications for population imaging through to emerging clinical practice. We found 66 whole brain structural MRI atlases world-wide. The vast majority were based on T1, T2, and/or proton density (PD) structural sequences, had been derived using parametric statistics (inappropriate for brain volume distributions), had limited supporting clinical or cognitive data, and included few younger (>5 and <18 years) or older (>60 years) subjects. To successfully characterize brain structural features and their changes across different stages of life, we conclude that whole brain structural MRI atlases should include: more subjects at the upper and lower extremes of age; additional structural sequences, including fluid attenuation inversion recovery (FLAIR) and T2* sequences; a range of appropriate statistics, e.g., rank-based or non-parametric; and detailed cognitive and clinical profiles of the included subjects in order to increase the relevance and utility of these atlases. PMID:28154532

  12. Toward the holistic, reference, and extendable atlas of the human brain, head, and neck.

    PubMed

    Nowinski, Wieslaw L

    2015-06-01

    Despite numerous efforts, a fairly complete (holistic) anatomical model of the whole, normal, adult human brain, which is required as the reference in brain studies and clinical applications, has not yet been constructed. Our ultimate objective is to build this kind of atlas from advanced in vivo imaging. This work presents the taxonomy of our currently developed brain atlases and addresses the design, content, functionality, and current results in the holistic atlas development as well as atlas usefulness and future directions. We have developed to date 35 commercial brain atlases (along with numerous research prototypes), licensed to 63 companies and institutions, and made available to medical societies, organizations, medical schools, and individuals. These atlases have been applied in education, research, and clinical applications. Hundreds of thousands of patients have been treated by using our atlases. Based on this experience, the first version of the holistic and reference atlas of the brain, head, and neck has been developed and made available. The atlas has been created from multispectral 3 and 7 Tesla and high-resolution CT in vivo scans. It is fully 3D, scalable, interactive, and highly detailed with about 3,000 labeled components. This atlas forms a foundation for the development of a multi-level molecular, cellular, anatomical, physiological, and behavioral brain atlas platform.

  13. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  14. Windows on the brain: the emerging role of atlases and databases in neuroscience

    NASA Technical Reports Server (NTRS)

    Van Essen, David C.; VanEssen, D. C. (Principal Investigator)

    2002-01-01

    Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

  15. A Four-Dimensional Probabilistic Atlas of the Human Brain

    PubMed Central

    Mazziotta, John; Toga, Arthur; Evans, Alan; Fox, Peter; Lancaster, Jack; Zilles, Karl; Woods, Roger; Paus, Tomas; Simpson, Gregory; Pike, Bruce; Holmes, Colin; Collins, Louis; Thompson, Paul; MacDonald, David; Iacoboni, Marco; Schormann, Thorsten; Amunts, Katrin; Palomero-Gallagher, Nicola; Geyer, Stefan; Parsons, Larry; Narr, Katherine; Kabani, Noor; Le Goualher, Georges; Feidler, Jordan; Smith, Kenneth; Boomsma, Dorret; Pol, Hilleke Hulshoff; Cannon, Tyrone; Kawashima, Ryuta; Mazoyer, Bernard

    2001-01-01

    The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders. PMID:11522763

  16. A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth.

    PubMed

    Gholipour, Ali; Rollins, Caitlin K; Velasco-Annis, Clemente; Ouaalam, Abdelhakim; Akhondi-Asl, Alireza; Afacan, Onur; Ortinau, Cynthia M; Clancy, Sean; Limperopoulos, Catherine; Yang, Edward; Estroff, Judy A; Warfield, Simon K

    2017-03-28

    Longitudinal characterization of early brain growth in-utero has been limited by a number of challenges in fetal imaging, the rapid change in size, shape and volume of the developing brain, and the consequent lack of suitable algorithms for fetal brain image analysis. There is a need for an improved digital brain atlas of the spatiotemporal maturation of the fetal brain extending over the key developmental periods. We have developed an algorithm for construction of an unbiased four-dimensional atlas of the developing fetal brain by integrating symmetric diffeomorphic deformable registration in space with kernel regression in age. We applied this new algorithm to construct a spatiotemporal atlas from MRI of 81 normal fetuses scanned between 19 and 39 weeks of gestation and labeled the structures of the developing brain. We evaluated the use of this atlas and additional individual fetal brain MRI atlases for completely automatic multi-atlas segmentation of fetal brain MRI. The atlas is available online as a reference for anatomy and for registration and segmentation, to aid in connectivity analysis, and for groupwise and longitudinal analysis of early brain growth.

  17. High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

    NASA Astrophysics Data System (ADS)

    Huang, Su; Lu, Zhongkang; Huang, Weimin; Seramani, Sankar; Ramasamy, Boominathan; Sekar, Sakthivel; Guan, Cuntai; Bhakoo, Kishore

    2016-03-01

    Image based atlases for rats brain have a significant impact on pre-clinical research. In this project we acquired T1-weighted images from Wistar rodent brains with fine 59μm isotropical resolution for generation of the atlas template image. By applying post-process procedures using a semi-automatic brain extraction method, we delineated the brain tissues from source data. Furthermore, we applied a symmetric group-wise normalization method to generate an optimized template of T1 image of rodent brain, then aligned our template to the Waxholm Space. In addition, we defined several simple and explicit landmarks to corresponding our template with the well known Paxinos stereotaxic reference system. Anchoring at the origin of the Waxholm Space, we applied piece-wise linear transformation method to map the voxels of the template into the coordinates system in Paxinos' stereotoxic coordinates to facilitate the labelling task. We also cross-referenced our data with both published rodent brain atlas and image atlases available online, methodologically labelling the template to produce a Wistar brain atlas identifying more than 130 structures. Particular attention was paid to the cortex and cerebellum, as these areas encompass the most researched aspects of brain functions. Moreover, we adopted the structure hierarchy and naming nomenclature common to various atlases, so that the names and hierarchy structure presented in the atlas are readily recognised for easy use. It is believed the atlas will present a useful tool in rodent brain functional and pharmaceutical studies.

  18. Tumor growth model for atlas based registration of pathological brain MR images

    NASA Astrophysics Data System (ADS)

    Moualhi, Wafa; Ezzeddine, Zagrouba

    2015-02-01

    The motivation of this work is to register a tumor brain magnetic resonance (MR) image with a normal brain atlas. A normal brain atlas is deformed in order to take account of the presence of a large space occupying tumor. The method use a priori model of tumor growth assuming that the tumor grows in a radial way from a starting point. First, an affine transformation is used in order to bring the patient image and the brain atlas in a global correspondence. Second, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. Finally, the seeded atlas is deformed combining a method derived from optical flow principles and a model for tumor growth (MTG). Results show that an automatic segmentation method of brain structures in the presence of large deformation can be provided.

  19. Automated Talairach atlas labels for functional brain mapping.

    PubMed

    Lancaster, J L; Woldorff, M G; Parsons, L M; Liotti, M; Freitas, C S; Rainey, L; Kochunov, P V; Nickerson, D; Mikiten, S A; Fox, P T

    2000-07-01

    An automated coordinate-based system to retrieve brain labels from the 1988 Talairach Atlas, called the Talairach Daemon (TD), was previously introduced [Lancaster et al., 1997]. In the present study, the TD system and its 3-D database of labels for the 1988 Talairach atlas were tested for labeling of functional activation foci. TD system labels were compared with author-designated labels of activation coordinates from over 250 published functional brain-mapping studies and with manual atlas-derived labels from an expert group using a subset of these activation coordinates. Automated labeling by the TD system compared well with authors' labels, with a 70% or greater label match averaged over all locations. Author-label matching improved to greater than 90% within a search range of +/-5 mm for most sites. An adaptive grey matter (GM) range-search utility was evaluated using individual activations from the M1 mouth region (30 subjects, 52 sites). It provided an 87% label match to Brodmann area labels (BA 4 & BA 6) within a search range of +/-5 mm. Using the adaptive GM range search, the TD system's overall match with authors' labels (90%) was better than that of the expert group (80%). When used in concert with authors' deeper knowledge of an experiment, the TD system provides consistent and comprehensive labels for brain activation foci. Additional suggested applications of the TD system include interactive labeling, anatomical grouping of activation foci, lesion-deficit analysis, and neuroanatomy education.

  20. Digital atlas of the zebra finch (Taeniopygia guttata) brain: a high-resolution photo atlas.

    PubMed

    Karten, Harvey J; Brzozowska-Prechtl, Agnieszka; Lovell, Peter V; Tang, Daniel D; Mello, Claudio V; Wang, Haibin; Mitra, Partha P

    2013-11-01

    We describe a set of new comprehensive, high-quality, high-resolution digital images of histological sections from the brain of male zebra finches (Taeniopygia guttata) and make them publicly available through an interactive website (http://zebrafinch.brainarchitecture.org/). These images provide a basis for the production of a dimensionally accurate and detailed digital nonstereotaxic atlas. Nissl- and myelin-stained brain sections are provided in the transverse, sagittal, and horizontal planes, with the transverse plane approximating the more traditional Frankfurt plane. In addition, a separate set of brain sections in this same plane is stained for tyrosine hydroxylase, revealing the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the songbird brain. For a subset of sagittal sections we also prepared a corresponding set of drawings, defining and annotating various nuclei, fields, and fiber tracts that are visible under Nissl and myelin staining. This atlas of the zebra finch brain is expected to become an important tool for birdsong research and comparative studies of brain organization and evolution.

  1. Quantitative analysis of brain pathology based on MRI and brain atlases--applications for cerebral palsy.

    PubMed

    Faria, Andreia V; Hoon, Alexander; Stashinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I; van Zijl, Peter C M; Mori, Susumu

    2011-02-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions.

  2. Atlas image labeling of subcortical structures and vascular territories in brain CT images.

    PubMed

    Du, Kaifang; Zhang, Li; Nguyen, Tony; Ordy, Vincent; Fichte, Heinz; Ditt, Hendrik; Chefd'hotel, Christophe

    2013-01-01

    We propose a multi-atlas labeling method for subcortical structures and cerebral vascular territories in brain CT images. Each atlas image is registered to the query image by a non-rigid registration and the deformation is then applied to the labeling of the atlas image to obtain the labeling of the query image. Four label fusion strategies (single atlas, most similar atlas, major voting, and STAPLE) were compared. Image similarity values in non-rigid registration were calculated and used to select and rank atlases. Major voting fusion strategy gave the best accuracy, with DSC (Dice similarity coefficient) around 0.85 ± 0.03 for caudate, putamen, and thalamus. The experimental results also show that fusing more atlases does not necessarily yield higher accuracy and we should be able to improve accuracy and decrease computation cost at the same time by selecting a preferred set with the minimum number of atlases.

  3. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

    PubMed

    Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

  4. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases

    PubMed Central

    Forbes, Jessica L.; Kim, Regina E. Y.; Paulsen, Jane S.; Johnson, Hans J.

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%. PMID:27536233

  5. Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline.

    PubMed

    Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

    2014-01-01

    Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual "atlases" that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures.

  6. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.

    PubMed

    Mikula, Shawn; Stone, James M; Jones, Edward G

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses.

  7. Regional growth and atlasing of the developing human brain

    PubMed Central

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V.; Edwards, A. David; Counsell, Serena J.; Rueckert, Daniel

    2016-01-01

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45 weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. PMID:26499811

  8. Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain.

    PubMed

    Veraart, Jelle; Leergaard, Trygve B; Antonsen, Bjørnar T; Van Hecke, Wim; Blockx, Ines; Jeurissen, Ben; Jiang, Yi; Van der Linden, Annemie; Johnson, G Allan; Verhoye, Marleen; Sijbers, Jan

    2011-10-15

    Rats are widely used in experimental neurobiological research, and rat brain atlases are important resources for identifying brain regions in the context of experimental microsurgery, tissue sampling, and neuroimaging, as well as comparison of findings across experiments. Currently, most available rat brain atlases are constructed from histological material derived from single specimens, and provide two-dimensional or three-dimensional (3D) outlines of diverse brain regions and fiber tracts. Important limitations of such atlases are that they represent individual specimens, and that finer details of tissue architecture are lacking. Access to more detailed 3D brain atlases representative of a population of animals is needed. Diffusion tensor imaging (DTI) is a unique neuroimaging modality that provides sensitive information about orientation structure in tissues, and is widely applied in basic and clinical neuroscience investigations. To facilitate analysis and assignment of location in rat brain neuroimaging investigations, we have developed a population-averaged three-dimensional DTI atlas of the normal adult Sprague Dawley rat brain. The atlas is constructed from high resolution ex vivo DTI images, which were nonlinearly warped into a population-averaged in vivo brain template. The atlas currently comprises a selection of manually delineated brain regions, the caudate-putamen complex, globus pallidus, entopeduncular nucleus, substantia nigra, external capsule, corpus callosum, internal capsule, cerebral peduncle, fimbria of the hippocampus, fornix, anterior commisure, optic tract, and stria terminalis. The atlas is freely distributed and potentially useful for several purposes, including automated and manual delineation of rat brain structural and functional imaging data.

  9. ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

    PubMed

    Grote, Steffi; Prüfer, Kay; Kelso, Janet; Dannemann, Michael

    2016-10-15

    We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages.

  10. Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

    NASA Astrophysics Data System (ADS)

    Mahfouz, Ahmed; Ziats, Mark N.; Rennert, Owen M.; Lelieveldt, Boudewijn P. F.; Reinders, Marcel J. T.

    2014-03-01

    The human brain comprises systems of networks that span the molecular, cellular, anatomic and functional levels. Molecular studies of the developing brain have focused on elucidating networks among gene products that may drive cellular brain development by functioning together in biological pathways. On the other hand, studies of the brain connectome attempt to determine how anatomically distinct brain regions are connected to each other, either anatomically (diffusion tensor imaging) or functionally (functional MRI and EEG), and how they change over development. A global examination of the relationship between gene expression and connectivity in the developing human brain is necessary to understand how the genetic signature of different brain regions instructs connections to other regions. Furthermore, analyzing the development of connectivity networks based on the spatio-temporal dynamics of gene expression provides a new insight into the effect of neurodevelopmental disease genes on brain networks. In this work, we construct connectivity networks between brain regions based on the similarity of their gene expression signature, termed "Genomic Connectivity Networks" (GCNs). Genomic connectivity networks were constructed using data from the BrainSpan Transcriptional Atlas of the Developing Human Brain. Our goal was to understand how the genetic signatures of anatomically distinct brain regions relate to each other across development. We assessed the neurodevelopmental changes in connectivity patterns of brain regions when networks were constructed with genes implicated in the neurodevelopmental disorder autism (autism spectrum disorder; ASD). Using graph theory metrics to characterize the GCNs, we show that ASD-GCNs are relatively less connected later in development with the cerebellum showing a very distinct expression of ASD-associated genes compared to other brain regions.

  11. Three-dimensional atlas of iron, copper, and zinc in the mouse cerebrum and brainstem.

    PubMed

    Hare, Dominic J; Lee, Jason K; Beavis, Alison D; van Gramberg, Amanda; George, Jessica; Adlard, Paul A; Finkelstein, David I; Doble, Philip A

    2012-05-01

    Atlases depicting molecular and functional features of the brain are becoming an integral part of modern neuroscience. In this study we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantitatively measure iron (Fe), copper (Cu), and zinc (Zn) levels in a serially sectioned C57BL/6 mouse brain (cerebrum and brainstem). Forty-six sections were analyzed in a single experiment of approximately 158 h in duration. We constructed a 46-plate reference atlas by aligning quantified images of metal distribution with corresponding coronal sections from the Allen Mouse Brain Reference Atlas. The 46 plates were also used to construct three-dimensional models of Fe, Cu, and Zn distribution. This atlas represents the first reconstruction of quantitative trace metal distribution through the brain by LA-ICPMS and will facilitate the study of trace metals in the brain and help to elucidate their role in neurobiology.

  12. A combined histological and MRI brain atlas of the common marmoset monkey, Callithrix jacchus

    PubMed Central

    Newman, John D.; Kenkel, William M.; Aronoff, Emily C.; Bock, Nicholas A.; Zametkin, Molly R.; Silva, Afonso C.

    2009-01-01

    The common marmoset, Callithrix jacchus, is of growing importance for research in neuroscience and related fields. In the present work, we describe a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. The histological sections and a simplified schematic atlas are available online at http://udn.nichd.nih.gov/brainatlas_home.html. PMID:19744521

  13. Localization and labeling of rat brain in MR image based on Paxinos-Watson atlas

    NASA Astrophysics Data System (ADS)

    Cao, Jie; Cai, Chao; Ding, Mingyue; Zhou, Chengping

    2006-03-01

    Localization and labeling of function regions in brain is an important topic in experimental brain sciences because the huge amount of data collected by neuroscientists will become meaningless if we cannot give them a precise description of their locations. In this paper, we proposed a localization and labelling method of 3D MR image of rat brain based on Paxinos-Watson atlas. Our objective is to use the specific atlas to accomplish localization and labeling of specified tissue of interest (TOI) to mimic a veteran expert such that invisible or unclear anatomic function regions in the MR images of rat brain can be automatically identified and marked. We proposed a multi-step method to locate and label the TOIs from the MR image of rat brain. Firstly, pre-processing. It aims at the digitization and 3D reconstruction of the atlas and MRI of rat brain. Secondly, two-step registration. The global registration is to eliminate the big misalign and section angle offset as well as the scale between the MRI and atlas. We can choose some unambiguous and characteristic points manually, and based on these correspondences a coarse registration is obtained using affine model. The local registration is to address individual variability of rat brain that can be performed by using Snake model. Thirdly, post-processing. The goal is to locate and label the TOIs in the selected MR image of rat brain slice guided by well-registered atlas. The experiments demonstrated the feasibility of our method.

  14. Atlas-based segmentation of pathological MR brain images using a model of lesion growth.

    PubMed

    Cuadra, Meritxell Bach; Pollo, Claudio; Bardera, Anton; Cuisenaire, Olivier; Villemure, Jean-Guy; Thiran, Jean-Philippe

    2004-10-01

    We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy.

  15. Automatic tissue segmentation of neonate brain MR Images with subject-specific atlases

    NASA Astrophysics Data System (ADS)

    Cherel, Marie; Budin, Francois; Prastawa, Marcel; Gerig, Guido; Lee, Kevin; Buss, Claudia; Lyall, Amanda; Zaldarriaga Consing, Kirsten; Styner, Martin

    2015-03-01

    Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions. We have developed a novel method that creates a probabilistic subject-specific atlas based on a population atlas currently containing a number of manually segmented cases. The generated subject-specific atlas is sharp and adapted to the subject that is being processed. We then segment brain tissue classes using the newly created atlas with a single-atlas expectation maximization based method. Our proposed method leads to a much lower failure rate in our experiments. The overall segmentation results are considerably improved when compared to using a non-subject-specific, population average atlas. Additionally, we have incorporated diffusion information obtained from Diffusion Tensor Images (DTI) to improve the detection of white matter that is not visible at this early age in structural MRI (sMRI) due to a lack of myelination. Although this necessitates the acquisition of an additional sequence, the diffusion information improves the white matter segmentation throughout the brain, especially for the mid-brain structures such as the corpus callosum and the internal capsule.

  16. A deformable digital brain atlas system according to Talairach and Tournoux.

    PubMed

    Ganser, Klaus A; Dickhaus, Hartmut; Metzner, Roland; Wirtz, Christian R

    2004-03-01

    Brain atlases are valuable tools which assist neurosurgeons during the planning of an intervention. Since a printed atlas book has several disadvantages-among them the difficulty to map the information onto a patient's individual anatomy-we have developed a digital version of the well-established stereotaxic brain atlas of Talairach and Tournoux. Our atlas system is mainly dedicated to assist neurosurgical planning, and its benefits are: (i) a three-dimensional (3D) representation of most brain structures contained in the Talairach atlas; (ii) a nonrigid matching capability which warps the standard atlas anatomy to an individual brain magnetic resonance imaging (MRI) dataset in a few minutes and which is able to take deformations due to tumors into account; (iii) the integration of several sources of neuroanatomical knowledge; (iv) an interface to a navigation system which allows utilization of atlas information intraoperatively. In this paper we outline the algorithm we have developed to achieve 3D surface models of the brain structures. Moreover, we describe the nonrigid matching method which consists of two tasks: firstly, point correspondences between the atlas and the patient are established in an automatic fashion, and secondly these displacement vectors are interpolated using a radial basis function approach to form a continuous transformation function. To generate appropriate target structures for the first of these tasks, we implemented a quick segmentation tool which is capable to segment the cortex and ventricles in less than 5 min. An evaluation shows that our nonrigid approach is more precise than the conventional piecewise linear matching, though it should be further improved for the region around the deep grey nuclei. Summarizing, we developed a Win32 program which permits the convenient and fast application of standardized anatomy to individual brains which potentially contain tumors.

  17. A multidimensional magnetic resonance histology atlas of the Wistar rat brain.

    PubMed

    Johnson, G Allan; Calabrese, Evan; Badea, Alexandra; Paxinos, George; Watson, Charles

    2012-09-01

    We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies.

  18. H. Julian Allen

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen stands beside the observation window of the 8 x 7 foot test section of the NACA Ames Unitary Plan Wind Tunnel. H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  19. Reconstruction of a 3D stereotactic brain atlas and its contour-to-contour elastic deformation

    NASA Astrophysics Data System (ADS)

    Kimura, Masahiko; Otsuki, Taisuke

    1993-06-01

    We describe a refined method for estimating the 3-D geometry of cerebral structures of a patient's brain from magnetic resonance (MR) images by adapting a 3-D atlas to the images. The 3-D atlas represents the figures of anatomical subdivisions of deep cerebral structures as series of contours reconstructed from a stereotactic printed atlas. The method correlates corresponding points and curve segments that are recognizable in both the atlas and the image, by elastically deforming the atlas two-dimensionally, while maintaining the point-to-point and contour-to-contour correspondence, until equilibrium is reached. We have used the method experimentally for a patient with Parkinson's disease, and successfully estimated the substructures of the thalamus to be treated.

  20. Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation.

    PubMed

    Roy, Snehashis; He, Qing; Sweeney, Elizabeth; Carass, Aaron; Reich, Daniel S; Prince, Jerry L; Pham, Dzung L

    2015-09-01

    Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject-specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole-brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available state-of-the art approaches.

  1. Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

    PubMed Central

    Chung, Ji Ryang; Sung, Chul; Mayerich, David; Kwon, Jaerock; Miller, Daniel E.; Huffman, Todd; Keyser, John; Abbott, Louise C.; Choe, Yoonsuck

    2011-01-01

    Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions. PMID:22275895

  2. 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

    PubMed Central

    Rumple, Ashley; McMurray, Matthew; Johns, Josephine; Lauder, Jean; Makam, Pooja; Radcliffe, Marlana; Oguz, Ipek

    2013-01-01

    Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community. PMID:23861758

  3. Atlas-based automatic mouse brain image segmentation revisited: model complexity vs. image registration.

    PubMed

    Bai, Jordan; Trinh, Thi Lan Huong; Chuang, Kai-Hsiang; Qiu, Anqi

    2012-07-01

    Although many atlas-based segmentation methods have been developed and validated for the human brain, limited work has been done for the mouse brain. This paper investigated roles of image registration and segmentation model complexity in the mouse brain segmentation. We employed four segmentation models [single atlas, multiatlas, simultaneous truth and performance level estimation (STAPLE) and Markov random field (MRF) via four different image registration algorithms (affine, B-spline free-form deformation (FFD), Demons and large deformation diffeomorphic metric mapping (LDDMM)] for delineating 19 structures from in vivo magnetic resonance microscopy images. We validated their accuracies against manual segmentation. Our results revealed that LDDMM outperformed Demons, FFD and affine in any of the segmentation models. Under the same registration, increasing segmentation model complexity from single atlas to multiatlas, STAPLE or MRF significantly improved the segmentation accuracy. Interestingly, the multiatlas-based segmentation using nonlinear registrations (FFD, Demons and LDDMM) had similar performance to their STAPLE counterparts, while they both outperformed their MRF counterparts. Furthermore, when the single-atlas affine segmentation was used as reference, the improvement due to nonlinear registrations (FFD, Demons and LDDMM) in the single-atlas segmentation model was greater than that due to increasing model complexity (multiatlas, STAPLE and MRF affine segmentation). Hence, we concluded that image registration plays a more crucial role in the atlas-based automatic mouse brain segmentation as compared to model complexity. Multiple atlases with LDDMM can best improve the segmentation accuracy in the mouse brain among all segmentation models tested in this study.

  4. Atlas-based segmentation of deep brain structures using non-rigid registration

    NASA Astrophysics Data System (ADS)

    Khan, Muhammad Faisal; Mewes, Klaus; Gross, Robert E.; Škrinjar, Oskar

    2008-03-01

    Deep brain structures are frequently used as targets in neurosurgical procedures. However, the boundaries of these structures are often not visible in clinically used MR and CT images. Techniques based on anatomical atlases and indirect targeting are used to infer the location of these targets intraoperatively. Initial errors of such approaches may be up to a few millimeters, which is not negligible. E.g. subthalamic nucleus is approximately 4x6 mm in the axial plane and the diameter of globus pallidus internus is approximately 8 mm, both of which are used as targets in deep brain stimulation surgery. To increase the initial localization accuracy of deep brain structures we have developed an atlas-based segmentation method that can be used for the surgery planning. The atlas is a high resolution MR head scan of a healthy volunteer with nine deep brain structures manually segmented. The quality of the atlas image allowed for the segmentation of the deep brain structures, which is not possible from the clinical MR head scans of patients. The subject image is non-rigidly registered to the atlas image using thin plate splines to represent the transformation and normalized mutual information as a similarity measure. The obtained transformation is used to map the segmented structures from the atlas to the subject image. We tested the approach on five subjects. The quality of the atlas-based segmentation was evaluated by visual inspection of the third and lateral ventricles, putamena, and caudate nuclei, which are visible in the subject MR images. The agreement of these structures for the five tested subjects was approximately 1 to 2 mm.

  5. Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings.

    PubMed

    Mahfouz, Ahmed; van de Giessen, Martijn; van der Maaten, Laurens; Huisman, Sjoerd; Reinders, Marcel; Hawrylycz, Michael J; Lelieveldt, Boudewijn P F

    2015-02-01

    The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization of these expression patterns. In this paper, we describe a non-linear embedding technique called Barnes-Hut Stochastic Neighbor Embedding (BH-SNE) that emphasizes the local similarity structure of high-dimensional data points. By applying BH-SNE to the gene expression data from the Allen Brain Atlases, we demonstrate the consistency of the 2D, non-linear embedding of the sagittal and coronal mouse brain atlases, and across 6 human brains. In addition, we quantitatively show that BH-SNE maps are superior in their separation of neuroanatomical regions in comparison to PCA and cMDS. Finally, we assess the effect of higher-order principal components on the global structure of the BH-SNE similarity maps. Based on our observations, we conclude that BH-SNE maps with or without prior dimensionality reduction (based on PCA) provide comprehensive and intuitive insights in both the local and global spatial transcriptome structure of the human and mouse Allen Brain Atlases.

  6. EPICS: Allen-Bradley hardware reference manual

    SciTech Connect

    Nawrocki, G.

    1993-04-05

    This manual covers the following hardware: Allen-Bradley 6008 -- SV VMEbus I/O scanner; Allen-Bradley universal I/O chassis 1771-A1B, -A2B, -A3B, and -A4B; Allen-Bradley power supply module 1771-P4S; Allen-Bradley 1771-ASB remote I/O adapter module; Allen-Bradley 1771-IFE analog input module; Allen-Bradley 1771-OFE analog output module; Allen-Bradley 1771-IG(D) TTL input module; Allen-Bradley 1771-OG(d) TTL output; Allen-Bradley 1771-IQ DC selectable input module; Allen-Bradley 1771-OW contact output module; Allen-Bradley 1771-IBD DC (10--30V) input module; Allen-Bradley 1771-OBD DC (10--60V) output module; Allen-Bradley 1771-IXE thermocouple/millivolt input module; and the Allen-Bradley 2705 RediPANEL push button module.

  7. A generative probability model of joint label fusion for multi-atlas based brain segmentation.

    PubMed

    Wu, Guorong; Wang, Qian; Zhang, Daoqiang; Nie, Feiping; Huang, Heng; Shen, Dinggang

    2014-08-01

    Automated labeling of anatomical structures in medical images is very important in many neuroscience studies. Recently, patch-based labeling has been widely investigated to alleviate the possible mis-alignment when registering atlases to the target image. However, the weights used for label fusion from the registered atlases are generally computed independently and thus lack the capability of preventing the ambiguous atlas patches from contributing to the label fusion. More critically, these weights are often calculated based only on the simple patch similarity, thus not necessarily providing optimal solution for label fusion. To address these limitations, we propose a generative probability model to describe the procedure of label fusion in a multi-atlas scenario, for the goal of labeling each point in the target image by the best representative atlas patches that also have the largest labeling unanimity in labeling the underlying point correctly. Specifically, sparsity constraint is imposed upon label fusion weights, in order to select a small number of atlas patches that best represent the underlying target patch, thus reducing the risks of including the misleading atlas patches. The labeling unanimity among atlas patches is achieved by exploring their dependencies, where we model these dependencies as the joint probability of each pair of atlas patches in correctly predicting the labels, by analyzing the correlation of their morphological error patterns and also the labeling consensus among atlases. The patch dependencies will be further recursively updated based on the latest labeling results to correct the possible labeling errors, which falls to the Expectation Maximization (EM) framework. To demonstrate the labeling performance, we have comprehensively evaluated our patch-based labeling method on the whole brain parcellation and hippocampus segmentation. Promising labeling results have been achieved with comparison to the conventional patch-based labeling

  8. A Web-based Brain Atlas of the Vervet Monkey, Chlorocebus aethiops

    PubMed Central

    Woods, Roger P.; Fears, Scott C.; Jorgensen, Matthew J.; Fairbanks, Lynn A.; Toga, Arthur W.; Freimer, Nelson B.

    2010-01-01

    Vervet monkeys are a frequently studied animal model in neuroscience research. Although equally distantly related to humans, the ancestors of vervets diverged from those of macaques and baboons more than eleven million years ago, antedating the divergence of the ancestors of humans, chimpanzees and gorillas. To facilitate anatomic localization in the vervet brain, two linked on-line electronic atlases are described, one based on registered MRI scans from hundreds of vervets (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetmratlas/vervetmratlas.html) and the other based on a high-resolution cryomacrotome study of a single vervet (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetatlas/vervetatlas.html). The averaged MRI atlas is also available as a volume in Neuroimaging Informatics Technology Initiative format. In the cryomacrotome atlas, various sulcal and subcortical structures have been anatomically labeled and surface rendered views are provided along the primary planes of section. Both atlases simultaneously provide views in all three primary planes of section, rapid navigation by clicking on the displayed images, and stereotaxic coordinates in the averaged MRI atlas space. Despite the extended time period since their divergence, the major sulcal and subcortical landmarks in vervets are highly conserved relative to those described in macaques. PMID:20923706

  9. Use of Brain MRI Atlases to Determine Boundaries of Age-Related Pathology: The Importance of Statistical Method

    PubMed Central

    Dickie, David Alexander; Job, Dominic E.; Gonzalez, David Rodriguez; Shenkin, Susan D.; Wardlaw, Joanna M.

    2015-01-01

    Introduction Neurodegenerative disease diagnoses may be supported by the comparison of an individual patient’s brain magnetic resonance image (MRI) with a voxel-based atlas of normal brain MRI. Most current brain MRI atlases are of young to middle-aged adults and parametric, e.g., mean ±standard deviation (SD); these atlases require data to be Gaussian. Brain MRI data, e.g., grey matter (GM) proportion images, from normal older subjects are apparently not Gaussian. We created a nonparametric and a parametric atlas of the normal limits of GM proportions in older subjects and compared their classifications of GM proportions in Alzheimer’s disease (AD) patients. Methods Using publicly available brain MRI from 138 normal subjects and 138 subjects diagnosed with AD (all 55–90 years), we created: a mean ±SD atlas to estimate parametrically the percentile ranks and limits of normal ageing GM; and, separately, a nonparametric, rank order-based GM atlas from the same normal ageing subjects. GM images from AD patients were then classified with respect to each atlas to determine the effect statistical distributions had on classifications of proportions of GM in AD patients. Results The parametric atlas often defined the lower normal limit of the proportion of GM to be negative (which does not make sense physiologically as the lowest possible proportion is zero). Because of this, for approximately half of the AD subjects, 25–45% of voxels were classified as normal when compared to the parametric atlas; but were classified as abnormal when compared to the nonparametric atlas. These voxels were mainly concentrated in the frontal and occipital lobes. Discussion To our knowledge, we have presented the first nonparametric brain MRI atlas. In conditions where there is increasing variability in brain structure, such as in old age, nonparametric brain MRI atlases may represent the limits of normal brain structure more accurately than parametric approaches. Therefore, we

  10. Multi-parametric analysis and registration of brain tumors: constructing statistical atlases and diagnostic tools of predictive value.

    PubMed

    Davatzikos, Christos; Zacharaki, Evangelia I; Gooya, Ali; Clark, Vanessa

    2011-01-01

    We discuss computer-based image analysis algorithms of multi-parametric MRI of brain tumors, aiming to assist in early diagnosis of infiltrating brain tumors, and to construct statistical atlases summarizing population-based characteristics of brain tumors. These methods combine machine learning, deformable registration, multi-parametric segmentation, and biophysical modeling of brain tumors.

  11. Automatic brain cropping and atlas slice matching using a PCNN and a generalized invariant Hough transform

    NASA Astrophysics Data System (ADS)

    Swathanthira Kumar, M. M.; Sullivan, John M., Jr.

    2007-03-01

    Medical research is dominated by animal models, especially rats and mice. Within a species most laboratory subjects exhibit little variation in brain anatomy. This uniformity of features is used to crop regions of interest based upon a known, cropped brain atlas. For any study involving N subjects, image registration or alignment to an atlas is required to construct a composite result. A highly resolved stack of T2 weighted MRI anatomy images of a Sprague-Dawley rat was registered and cropped to a known segmented atlas. This registered MRI volume was used as the reference atlas. A Pulse Coupled Neural Network (PCNN) was used to separate brain tissue from surrounding structures, such as cranium and muscle. Each iteration of the PCNN produces binary images of increasing area as the intensity spectrum is increased. A rapid filtering algorithm is applied that breaks narrow passages connecting larger segmented areas. A Generalized Invariant Hough Transform is applied subsequently to each PCNN segmented area to identify which segmented reference slice it matches. This process is repeated for multiple slices within each subject. Since we have apriori knowledge of the image ordering and fields of view this information provides initial estimates for subsequent registration codes. This process of subject slice extraction to PCNN mask creations and GIHT matching with known atlas locations is fully automatic.

  12. High-resolution digital brain atlases: a Hubble telescope for the brain.

    PubMed

    Jones, Edward G; Stone, James M; Karten, Harvey J

    2011-05-01

    We describe implementation of a method for digitizing at microscopic resolution brain tissue sections containing normal and experimental data and for making the content readily accessible online. Web-accessible brain atlases and virtual microscopes for online examination can be developed using existing computer and internet technologies. Resulting databases, made up of hierarchically organized, multiresolution images, enable rapid, seamless navigation through the vast image datasets generated by high-resolution scanning. Tools for visualization and annotation of virtual microscope slides enable remote and universal data sharing. Interactive visualization of a complete series of brain sections digitized at subneuronal levels of resolution offers fine grain and large-scale localization and quantification of many aspects of neural organization and structure. The method is straightforward and replicable; it can increase accessibility and facilitate sharing of neuroanatomical data. It provides an opportunity for capturing and preserving irreplaceable, archival neurohistological collections and making them available to all scientists in perpetuity, if resources could be obtained from hitherto uninterested agencies of scientific support.

  13. A Unified Framework for Cross-modality Multi-atlas Segmentation of Brain MRI

    PubMed Central

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Leemput, Koen Van

    2013-01-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion. PMID:24001931

  14. A unified framework for cross-modality multi-atlas segmentation of brain MRI.

    PubMed

    Eugenio Iglesias, Juan; Rory Sabuncu, Mert; Van Leemput, Koen

    2013-12-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion.

  15. Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression.

    PubMed

    Serag, Ahmed; Aljabar, Paul; Ball, Gareth; Counsell, Serena J; Boardman, James P; Rutherford, Mary A; Edwards, A David; Hajnal, Joseph V; Rueckert, Daniel

    2012-02-01

    Medical imaging has shown that, during early development, the brain undergoes more changes in size, shape and appearance than at any other time in life. A better understanding of brain development requires a spatio-temporal atlas that characterizes the dynamic changes during this period. In this paper we present an approach for constructing a 4D atlas of the developing brain, between 28 and 44 weeks post-menstrual age at time of scan, using T1 and T2 weighted MR images from 204 premature neonates. The method used for the creation of the average 4D atlas utilizes non-rigid registration between all pairs of images to eliminate bias in the atlas toward any of the original images. In addition, kernel regression is used to produce age-dependent anatomical templates. A novelty in our approach is the use of a time-varying kernel width, to overcome the variations in the distribution of subjects at different ages. This leads to an atlas that retains a consistent level of detail at every time-point. Comparisons between the resulting atlas and atlases constructed using affine and non-rigid registration are presented. The resulting 4D atlas has greater anatomic definition than currently available 4D atlases created using various affine and non-rigid registration approaches, an important factor in improving registrations between the atlas and individual subjects. Also, the resulting 4D atlas can serve as a good representative of the population of interest as it reflects both global and local changes. The atlas is publicly available at www.brain-development.org.

  16. Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus).

    PubMed

    Tokuno, Hironobu; Tanaka, Ikuko; Umitsu, Yoshitomo; Akazawa, Toshikazu; Nakamura, Yasuhisa

    2009-05-01

    Here we describe a web-accessible digital brain atlas of the common marmoset (Callithrix jacchus) at http://marmoset-brain.org:2008. We prepared the histological sections of the marmoset brain using various staining techniques. For virtual microscopy, high-resolution digital images of sections were obtained with Aperio Scanscope. The digital images were then converted to Zoomify files (zoomable multiresolution image files). Thereby, we could provide the multiresolution images of the marmoset brains for fast interactive viewing on the web via the Internet. In addition, we describe an automated method to obtain drawings of Nissl-stained sections.

  17. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood.

    PubMed

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G; Anblagan, Devasuda; Telford, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Macnaught, Gillian; Semple, Scott I; Bastin, Mark E; Boardman, James P

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39(+5) weeks, range 37(+2)-41(+6)). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development.

  18. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood

    PubMed Central

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G.; Anblagan, Devasuda; Telford, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Macnaught, Gillian; Semple, Scott I.; Bastin, Mark E.; Boardman, James P.

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39+5 weeks, range 37+2–41+6). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development. PMID:27242423

  19. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain

    PubMed Central

    Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient’s age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results. PMID:26751577

  20. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain.

    PubMed

    Parisot, Sarah; Darlix, Amélie; Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient's age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results.

  1. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    PubMed

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc.

  2. Construction of a deformable spatiotemporal MRI atlas of the fetal brain: evaluation of similarity metrics and deformation models.

    PubMed

    Gholipour, Ali; Limperopoulos, Catherine; Clancy, Sean; Clouchoux, Cedric; Akhondi-Asl, Alireza; Estroff, Judy A; Warfield, Simon K

    2014-01-01

    The development and identification of best methods in fetal brain MRI analysis is crucial as we expect an outburst of studies on groupwise and longitudinal analysis of early brain development in the upcoming years. To address this critical need, in this paper, we have developed a mathematical framework for the construction of an unbiased deformable spatiotemporal atlas of the fetal brain MRI and compared it to alternative configurations in terms of similarity metrics and deformation models. Our contributions are twofold: first we suggest a novel approach to fetal brain spatiotemporal atlas construction that shows high capability in capturing anatomic variation between subjects; and second, within our atlas construction framework we evaluate and compare a set of plausible configurations for inter-subject fetal brain MRI registration and identify the most accurate approach that can potentially lead to most accurate results in population atlas construction, atlas-based segmentation, and group analysis. Our evaluation results indicate that symmetric diffeomorphic deformable registration with cross correlation similarity metric outperforms other configurations in this application and results in sharp unbiased atlases that can be used in fetal brain MRI analysis.

  3. A review of Edward Flatau's 1894 Atlas of the Human Brain by the neurologist Sigmund Freud.

    PubMed

    Triarhou, Lazaros C

    2011-01-01

    In 1894, the Polish neurologist Edward Flatau (1868-1932), working in Berlin, published an exquisite photographic atlas of the unfixed human brain, preceding by 2 years Das Menschenhirn, the reference work of Gustaf Retzius (1842-1919) in Stockholm. In his early career as a neuroanatomist and neurologist, Sigmund Freud (1856-1939) wrote a review of Flatau's atlas for the Internationale klinische Rundschau, which has not been included in the 'Standard Edition of the Complete Psychological Works'. The aim of the present paper is twofold: to document Freud's review, and to revive the largely forgotten atlas of Flatau. The full text of Freud is presented in translation. Further, one element Flatau, Retzius and Freud had in common is discussed: their early role as protagonists and firm supporters of Ramón y Cajal's neuron theory, the cornerstone of modern neuroscience.

  4. Implementation of talairach atlas based automated brain segmentation for radiation therapy dosimetry.

    PubMed

    Popple, R A; Griffith, H R; Sawrie, S M; Fiveash, J B; Brezovich, I A

    2006-02-01

    Radiotherapy for brain cancer inevitably results in irradiation of uninvolved brain. While it has been demonstrated that irradiation of the brain can result in cognitive deficits, dose-volume relationships are not well established. There is little work correlating a particular cognitive deficit with dose received by the region of the brain responsible for the specific cognitive function. One obstacle to such studies is that identification of brain anatomy is both labor intensive and dependent on the individual performing the segmentation. Automatic segmentation has the potential to be both efficient and consistent. Brains2 is a software package developed by the University of Iowa for MRI volumetric studies. It utilizes MR images, the Talairach atlas, and an artificial neural network (ANN) to segment brain images into substructures in a standardized manner. We have developed a software package, Brains2DICOM, that converts the regions of interest identified by Brains2 into a DICOM radiotherapy structure set. The structure set can be imported into a treatment planning system for dosimetry. We demonstrated the utility of Brains2DICOM using a test case, a 34-year-old man with diffuse astrocytoma treated with three-dimensional conformal radiotherapy. Brains2 successfully applied the Talairach atlas to identify the right and left frontal, parietal, temporal, occipital, subcortical, and cerebellum regions. Brains2 was not successful in applying the ANN to identify small structures, such as the hippocampus and caudate. Further work is necessary to revise the ANN or to develop new methods for identification of small structures in the presence of disease and radiation induced changes. The segmented regions-of-interest were transferred to our commercial treatment planning system using DICOM and dose-volume histograms were constructed. This method will facilitate the acquisition of data necessary for the development of normal tissue complication probability (NTCP) models that

  5. The brain of the common vampire bat, Desmodus rotundus murinus (Wagner, 1840): a cytoarchitectural atlas.

    PubMed

    Bhatnagar, K P

    2008-08-01

    The vampire bat, Desmodus rotundus, is exceptionally agile and stealthy in nature. Feeding at night on cattle blood, it is a known scourge carrying rabies. It is endowed with a very high neocortical volume among bats, acute olfactory capabilities and an accessory olfactory system. These characteristics have resulted into an impressive number of neuroanatomical investigations except a long due atlas on its brain. This study presents a cytoarchitectural atlas of the brain of the common vampire, Desmodus rotundus murinus, in the frontal plane, serially between the olfactory bulb and the medulla oblongata. Twenty six selected sections are presented, each separated by about 300 to 560 microns. The atlas figures show lugol fast blue-cresyl echt violet stained hemisections with their matching half in a labeled line drawing. About 595 discrete brain structures (some repeating) have been identified. This study is likely to provide the accurate localization of nuclear groups, whole structures, fiber tracts, and interconnections to facilitate future neuroanatomical and neurophysiological investigations on the vampire brain.

  6. A 3-dimensional digital atlas of the ascending sensory and the descending motor systems in the pigeon brain.

    PubMed

    Güntürkün, Onur; Verhoye, Marleen; De Groof, Geert; Van der Linden, Annemie

    2013-01-01

    Pigeons are classic animal models for learning, memory, and cognition. The majority of the current understanding about avian neurobiology outside of the domain of the song system has been established using pigeons. Since MRI represents an increasingly relevant tool for comparative neuroscience, a 3-dimensional MRI-based atlas of the pigeon brain becomes essential. Using multiple imaging protocols, we delineated diverse ascending sensory and descending motor systems as well as the hippocampal formation. This pigeon brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. In addition, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. This pigeon brain atlas is freely available for the scientific community.

  7. A Bayesian approach to the creation of a study-customized neonatal brain atlas.

    PubMed

    Zhang, Yajing; Chang, Linda; Ceritoglu, Can; Skranes, Jon; Ernst, Thomas; Mori, Susumu; Miller, Michael I; Oishi, Kenichi

    2014-11-01

    Atlas-based image analysis (ABA), in which an anatomical "parcellation map" is used for parcel-by-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain development, aging, and various diseases. The parcellation maps are often created based on common MRI templates, which allow users to transform the template to target images, or vice versa, to perform parcel-by-parcel statistics, and report the scientific findings based on common anatomical parcels. The use of a study-specific template, which represents the anatomical features of the study population better than common templates, is preferable for accurate anatomical labeling; however, the creation of a parcellation map for a study-specific template is extremely labor intensive, and the definitions of anatomical boundaries are not necessarily compatible with those of the common template. In this study, we employed a volume-based template estimation (VTE) method to create a neonatal brain template customized to a study population, while keeping the anatomical parcellation identical to that of a common MRI atlas. The VTE was used to morph the standardized parcellation map of the JHU-neonate-SS atlas to capture the anatomical features of a study population. The resultant "study-customized" T1-weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS atlas, in terms of the registration accuracy. A pronounced increase in the accuracy of cortical parcellation and superior tensor alignment were observed when the customized template was used. With the customized atlas-based analysis, the fractional anisotropy (FA) detected closely approximated the manual measurements. This tool provides a solution for achieving normalization-based measurements with increased accuracy, while reporting scientific findings in a consistent framework.

  8. Creation of a whole brain short association bundle atlas using a hybrid approach.

    PubMed

    Guevara, M; Roman, C; Houenou, J; Duclap, D; Poupon, C; Mangin, J-F; Guevara, P; Guevara, M; Roman, C; Houenou, J; Duclap, D; Poupon, C; Mangin, J-F; Guevara, P; Mangin, J-F; Roman, C; Duclap, D; Poupon, C; Houenou, J; Guevara, P; Guevara, M

    2016-08-01

    The Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of pathogenesis triggered by abnormal connectivity. In this work we expanded a previously developed method for the automatic creation of a whole brain SWM bundle atlas. The method is based on a hybrid approach. First a cortical parcellation is used to extract fibers connecting two regions. Then an intra-and inter-subject hierarchical clustering are applied to find well-defined SWM bundles reproducible across subjects. In addition to the fronto-parietal and insula regions of the left hemisphere, the analysis was extended to the temporal and occipital lobes, including all their internal regions, for both hemispheres. Validation steps are performed in order to test the robustness of the method and the reproducibility of the obtained bundles. First the method was applied to two independent groups of subjects, in order to discard bundles without match across the two independent atlases. Then, the resulting intersection atlas was projected on a third independent group of subjects in order to filter out bundles without reproducible and reliable projection. The final multi-subject U-fiber atlas is composed of 100 bundles in total, 50 per hemisphere, from which 35 are common to both hemispheres. The atlas can be used in clinical studies for segmentation of the SWM bundles in new subjects, and measure DW values or complement functional data.

  9. Atlas-based Segmentation of Developing Tissues in the Human Brain with Quantitative Validation in Young Fetuses

    PubMed Central

    Habas, Piotr A.; Kim, Kio; Rousseau, Francois; Glenn, Orit A.; Barkovich, A. James; Studholme, Colin

    2011-01-01

    Imaging of the human fetus using magnetic resonance (MR) is an essential tool for quantitative studies of normal as well as abnormal brain development in utero. However, because of fundamental differences in tissue types, tissue properties and tissue distribution between the fetal and adult brain, automated tissue segmentation techniques developed for adult brain anatomy are unsuitable for this data. In this paper, we describe methodology for automatic atlas-based segmentation of individual tissue types in motion-corrected 3D volumes reconstructed from clinical MR scans of the fetal brain. To generate anatomically correct automatic segmentations, we create a set of accurate manual delineations and build an in utero 3D statistical atlas of tissue distribution incorporating developing grey and white matter as well as transient tissue types such as the germinal matrix. The probabilistic atlas is associated with an unbiased average shape and intensity template for registration of new subject images to the space of the atlas. Quantitative whole brain 3D validation of tissue labeling performed on a set of 14 fetal MR scans (20.57–22.86 weeks gestational age) demonstrates that this atlas-based EM segmentation approach achieves consistently high DSC performance for the main tissue types in the fetal brain. This work indicates that reliable measures of brain development can be automatically derived from clinical MR imaging and opens up possibility of further 3D volumetric and morphometric studies with multiple fetal subjects. PMID:20108226

  10. A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

    PubMed

    Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

  11. A Three-Dimensional Stereotaxic MRI Brain Atlas of the Cichlid Fish Oreochromis mossambicus

    PubMed Central

    Simões, José M.; Teles, Magda C.; Oliveira, Rui F.; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system. PMID:22984463

  12. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

    NASA Astrophysics Data System (ADS)

    Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

    2014-03-01

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  13. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus.

    PubMed

    Gao, Yurui; Khare, Shweta P; Panda, Swetasudha; Choe, Ann S; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A

    2014-03-13

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include T2 structural imaging and diffusion tensor imaging. Ex vivo MRI acquisitions include T2 structural imaging and diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  14. New experimental results in atlas-based brain morphometry

    NASA Astrophysics Data System (ADS)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  15. A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis.

    PubMed

    Nie, Binbin; Chen, Kewei; Zhao, Shujun; Liu, Junhua; Gu, Xiaochun; Yao, Qunli; Hui, Jiaojie; Zhang, Zhijun; Teng, Gaojun; Zhao, Chunjie; Shan, Baoci

    2013-06-01

    This study constructs a rat brain T2 -weighted magnetic resonance imaging template including olfactory bulb and a compatible digital atlas. The atlas contains 624 carefully delineated brain structures based on the newest (2005) edition of rat brain atlas by Paxinos and Watson. An automated procedure, as an SPM toolbox, was introduced for spatially normalizing individual rat brains, conducting statistical analysis and visually localizing the results in the Atlas coordinate space. The brain template/atlas and the procedure were evaluated using functional images between rats with the right side middle cerebral artery occlusion (MCAO) and normal controls. The result shows that the brain region with significant signal decline in the MCAO rats was consistent with the occlusion position.

  16. Robust methods to create ex vivo minimum deformation atlases for brain mapping.

    PubMed

    Janke, Andrew L; Ullmann, Jeremy F P

    2015-02-01

    Highly detailed ex vivo 3D atlases of average structure are of critical importance to neuroscience and its current push to understanding the global microstructure of the brain. Multiple single slice histology sections can no longer provide sufficient detail of inter-slice microstructure and lack out of plane resolution. Two ex vivo methods have emerged that can create such detailed models. High-field micro MRI with the addition of contrast media has allowed intact whole brain microstructure imaging with an isotropic resolution of 15 μm in mouse. Blockface imaging has similarly evolved to a point where it is now possible to image an entire brain in a rigorous fashion with an out of plane resolution of 10 μm. Despite the destruction of the tissue as part of this process it allows a reconstructed model that is free from cutting artifacts. Both of these methods have been utilised to create minimum deformation atlases that are representative of the respective populations. The MDA atlases allow us unprecedented insight into the commonality and differences in microstructure in cortical structures in specific taxa. In this paper we provide an overview of how to create such MDA models from ex vivo data.

  17. Hybrid atlas-based and image-based approach for segmenting 3D brain MRIs

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2001-07-01

    This work is a contribution to the problem of localizing key cerebral structures in 3D MRIs and its quantitative evaluation. In pursuing it, the cooperation between an image-based segmentation method and a hierarchical deformable registration approach has been considered. The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions of an image, I(s), from the data set are identified. These regions, M(I), are obtained combining information from deformable atlas, achieved by the warping of eight previous labeled maps on I(s). Then, the goal of the decision stage is to precisely locate the contours of the 3D regions set by the markers. This contour decision is performed by a 3D extension of the watershed transform. The anatomical structures taken into consideration and embedded into the atlas are brain, ventricles, corpus callosum, cerebellum, right and left hippocampus, medulla and midbrain. The hybrid method operates fully automatically and in 3D, successfully providing segmented brain structures. The quality of the segmentation has been studied in terms of the detected volume ratio by using kappa statistic and ROC analysis. Results of the method are shown and validated on a 3D MRI phantom. This study forms part of an on-going long term research aiming at the creation of a 3D probabilistic multi-purpose anatomical brain atlas.

  18. Implementation of nonlinear registration of brain atlas based on piecewise grid system

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Gu, Lixu; Xu, Jianrong

    2007-12-01

    In this paper, a multi-step registration method of brain atlas and clinical Magnetic Resonance Imaging (MRI) data based on Thin-Plate Splines (TPS) and Piecewise Grid System (PGS) is presented. The method can help doctors to determine the corresponding anatomical structure between patient image and the brain atlas by piecewise nonlinear registration. Since doctors mostly pay attention to particular Region of Interest (ROI), and a global nonlinear registration is quite time-consuming which is not suitable for real-time clinical application, we propose a novel method to conduct linear registration in global area before nonlinear registration is performed in selected ROI. The homogenous feature points are defined to calculate the transform matrix between patient data and the brain atlas to conclude the mapping function. Finally, we integrate the proposed approach into an application of neurosurgical planning and guidance system which lends great efficiency in both neuro-anatomical education and guiding of neurosurgical operations. The experimental results reveal that the proposed approach can keep an average registration error of 0.25mm in near real-time manner.

  19. PCA and level set based non-rigid image registration for MRI and Paxinos-Watson atlas of rat brain

    NASA Astrophysics Data System (ADS)

    Cai, Chao; Liu, Ailing; Ding, Mingyue; Zhou, Chengping

    2007-12-01

    Image registration provides the ability to geometrically align one dataset with another. It is a basic task in a great variety of biomedical imaging applications. This paper introduced a novel three-dimensional registration method for Magnetic Resonance Image (MRI) and Paxinos-Watson Atlas of rat brain. For the purpose of adapting to a large range and non-linear deformation between MRI and atlas in higher registration accuracy, based on the segmentation of rat brain, we chose the principle components analysis (PCA) automatically performing the linear registration, and then, a level set based nonlinear registration correcting some small distortions. We implemented this registration method in a rat brain 3D reconstruction and analysis system. Experiments have demonstrated that this method can be successfully applied to registering the low resolution and noise affection MRI with Paxinos-Watson Atlas of rat brain.

  20. In vivo DTI tractography of the rat brain: an atlas of the main tracts in Paxinos space with histological comparison.

    PubMed

    Figini, Matteo; Zucca, Ileana; Aquino, Domenico; Pennacchio, Paolo; Nava, Simone; Di Marzio, Alessandro; Preti, Maria Giulia; Baselli, Guseppe; Spreafico, Roberto; Frassoni, Carolina

    2015-04-01

    Diffusion tensor imaging (DTI) is a magnetic resonance modality that permits to characterize the orientation and integrity of white matter (WM). DTI-based tractography techniques, allowing the virtual reconstruction of WM tract pathways, have found wide application in preclinical neurological research. Recently, anatomically detailed rat brain atlases including DTI data were constructed from ex vivo DTI images, but tractographic atlases of normal rats in vivo are still lacking. We propose here a probabilistic tractographic atlas of the main WM tracts in the healthy rat brain based on in vivo DTI acquisition. Our study was carried out on 10 adult female Sprague-Dawley rats using a 7T preclinical scanner. The MRI protocol permitted a reliable reconstruction of the main rat brain bundles: corpus callosum, cingulum, external capsule, internal capsule, anterior commissure, optic tract. The reconstructed fibers were compared with histological data, proving the viability of in vivo DTI tractography in the rat brain with the proposed acquisition and processing protocol. All the data were registered to a rat brain template in the coordinate system of the commonly used atlas by Paxinos and Watson; then the individual tracts were binarized and averaged, obtaining a probabilistic atlas in Paxinos-Watson space of the main rat brain WM bundles. With respect to the recent high-resolution MRI atlases, the resulting tractographic atlas, available online, provides complementary information about the average anatomical position of the considered WM tracts and their variability between normal animals. Furthermore, reference values for the main DTI-derived parameters, mean diffusivity and fractional anisotropy, were provided. Both these results can be used as references in preclinical studies on pathological rat models involving potential alterations of WM.

  1. A Spatio-Temporal Atlas of the Human Fetal Brain with Application to Tissue Segmentation

    PubMed Central

    Habas, Piotr A.; Kim, Kio; Rousseau, Francois; Glenn, Orit A.; Barkovich, A. James; Studholme, Colin

    2012-01-01

    Modeling and analysis of MR images of the early developing human brain is a challenge because of the transient nature of different tissue classes during brain growth. To address this issue, a statistical model that can capture the spatial variation of structures over time is needed. Here, we present an approach to building a spatio-temporal model of tissue distribution in the developing brain which can incorporate both developed tissues as well as transient tissue classes such as the germinal matrix by using constrained higher order polynomial models. This spatio-temporal model is created from a set of manual segmentations through groupwise registration and voxelwise non-linear modeling of tissue class membership, that allows us to represent the appearance as well as disappearance of the transient brain structures over time. Applying this model to atlas-based segmentation, we generate age-specific tissue probability maps and use them to initialize an EM segmentation of the fetal brain tissues. The approach is evaluated using clinical MR images of young fetuses with gestational ages ranging from 20.57 to 24.71 weeks. Results indicate improvement in performance of atlas-based EM segmentation provided by higher order temporal models that capture the variation of tissue occurrence over time. PMID:20425999

  2. Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete correspondences

    NASA Astrophysics Data System (ADS)

    Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

    2016-03-01

    The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra- subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool.

  3. Multi-Object Model-based Multi-Atlas Segmentation for Rodent Brains using Dense Discrete Correspondences

    PubMed Central

    Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

    2016-01-01

    The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra-subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool. PMID:27065200

  4. Brain tissue segmentation in PET-CT images using probabilistic atlas and variational Bayes inference.

    PubMed

    Xia, Yong; Wang, Jiabin; Eberl, Stefan; Fulham, Michael; Feng, David Dagan

    2011-01-01

    PET-CT provides aligned anatomical (CT) and functional (PET) images in a single scan, and has the potential to improve brain PET image segmentation, which can in turn improve quantitative clinical analyses. We propose a statistical segmentation algorithm that incorporates the prior anatomical knowledge represented by probabilistic brain atlas into the variational Bayes inference to delineate gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) in brain PET-CT images. Our approach adds an additional novel aspect by allowing voxels to have variable and adaptive prior probabilities of belonging to each class. We compared our algorithm to the segmentation approaches implemented in the expectation maximization segmentation (EMS) and statistical parametric mapping (SPM8) packages in 26 clinical cases. The results show that our algorithm improves the accuracy of brain PET-CT image segmentation.

  5. Dense deformation field estimation for atlas-based segmentation of pathological MR brain images.

    PubMed

    Bach Cuadra, M; De Craene, M; Duay, V; Macq, B; Pollo, C; Thiran, J-Ph

    2006-12-01

    Atlas registration is a recognized paradigm for the automatic segmentation of normal MR brain images. Unfortunately, atlas-based segmentation has been of limited use in presence of large space-occupying lesions. In fact, brain deformations induced by such lesions are added to normal anatomical variability and they may dramatically shift and deform anatomically or functionally important brain structures. In this work, we chose to focus on the problem of inter-subject registration of MR images with large tumors, inducing a significant shift of surrounding anatomical structures. First, a brief survey of the existing methods that have been proposed to deal with this problem is presented. This introduces the discussion about the requirements and desirable properties that we consider necessary to be fulfilled by a registration method in this context: To have a dense and smooth deformation field and a model of lesion growth, to model different deformability for some structures, to introduce more prior knowledge, and to use voxel-based features with a similarity measure robust to intensity differences. In a second part of this work, we propose a new approach that overcomes some of the main limitations of the existing techniques while complying with most of the desired requirements above. Our algorithm combines the mathematical framework for computing a variational flow proposed by Hermosillo et al. [G. Hermosillo, C. Chefd'Hotel, O. Faugeras, A variational approach to multi-modal image matching, Tech. Rep., INRIA (February 2001).] with the radial lesion growth pattern presented by Bach et al. [M. Bach Cuadra, C. Pollo, A. Bardera, O. Cuisenaire, J.-G. Villemure, J.-Ph. Thiran, Atlas-based segmentation of pathological MR brain images using a model of lesion growth, IEEE Trans. Med. Imag. 23 (10) (2004) 1301-1314.]. Results on patients with a meningioma are visually assessed and compared to those obtained with the most similar method from the state-of-the-art.

  6. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    NASA Astrophysics Data System (ADS)

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; MacNaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-03-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  7. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.

    PubMed

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P

    2016-03-24

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  8. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    PubMed Central

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-01-01

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  9. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    SciTech Connect

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-02-15

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI-LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  10. Three-dimensional average-shape atlas of the honeybee brain and its applications.

    PubMed

    Brandt, Robert; Rohlfing, Torsten; Rybak, Jürgen; Krofczik, Sabine; Maye, Alexander; Westerhoff, Malte; Hege, Hans-Christian; Menzel, Randolf

    2005-11-07

    The anatomical substrates of neural nets are usually composed from reconstructions of neurons that were stained in different preparations. Realistic models of the structural relationships between neurons require a common framework. Here we present 3-D reconstructions of single projection neurons (PN) connecting the antennal lobe (AL) with the mushroom body (MB) and lateral horn, groups of intrinsic mushroom body neurons (type 5 Kenyon cells), and a single mushroom body extrinsic neuron (PE1), aiming to compose components of the olfactory pathway in the honeybee. To do so, we constructed a digital standard atlas of the bee brain. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The results were qualitatively evaluated by generating average gray-value images corresponding to the average label images and judging the level of detail within the labeled regions. We found that the first affine registration step in the sequence results in a blurred image because of considerable local shape differences. However, already the first nonrigid iteration in the sequence corrected for most of the shape differences among individuals, resulting in images rich in internal detail. A second iteration improved on that somewhat and was selected as the standard. Registering neurons from different preparations into the standard atlas reveals 1) that the m-ACT neuron occupies the entire glomerulus (cortex and core) and overlaps with a local interneuron in the cortical layer; 2) that, in the MB calyces and the lateral horn of the protocerebral lobe, the axon terminals of two identified m-ACT neurons arborize in separate but close areas of the neuropil; and 3) that MB-intrinsic clawed Kenyon cells (type 5), with somata

  11. Automatic macroscopic density artefact removal in a Nissl-stained microscopic atlas of whole mouse brain.

    PubMed

    Ding, W; Li, A; Wu, J; Yang, Z; Meng, Y; Wang, S; Gong, H

    2013-08-01

    Acquiring a whole mouse brain at the micrometer scale is a complex, continuous and time-consuming process. Because of defects caused by sample preparation and microscopy, the acquired image data sets suffer from various macroscopic density artefacts that worsen the image quality. We have to develop the available preprocessing methods to improve image quality by removing the artefacts that effect cell segmentation, vascular tracing and visualization. In this study, a set of automatic artefact removal methods is proposed for images obtained by tissue staining and optical microscopy. These methods significantly improve the complicated images that contain various structures, including cells and blood vessels. The whole mouse brain data set with Nissl staining was tested, and the intensity of the processed images was uniformly distributed throughout different brain areas. Furthermore, the processed image data set with its uniform brightness and high quality is now a fundamental atlas for image analysis, including cell segmentation, vascular tracing and visualization.

  12. Atlasing location, asymmetry and inter-subject variability of white matter tracts in the human brain with MR diffusion tractography.

    PubMed

    Thiebaut de Schotten, Michel; Ffytche, Dominic H; Bizzi, Alberto; Dell'Acqua, Flavio; Allin, Matthew; Walshe, Muriel; Murray, Robin; Williams, Steven C; Murphy, Declan G M; Catani, Marco

    2011-01-01

    The purpose of this study is to create a white matter atlas of the human brain using diffusion tensor imaging (DTI) tractography and to describe the constant and variable features of the major pathways. DTI was acquired from 40 healthy right-handed adults and reconstructed tracts mapped within a common reference space (MNI). Group effect maps of each tract defined constant anatomical features while overlap maps were generated to study inter-subject variability and to compare DTI derived anatomy with a histological atlas. Two patients were studied to assess the localizing validity of the atlas. The DTI-derived maps are overall consistent with a previously published histological atlas. A statistically significant leftward asymmetry was found for the volume and number of streamlines of the cortico-spinal tract and the direct connections between Broca's and Wernicke's territories (long segment). A statistically significant rightward asymmetry was found for the inferior fronto-occipital fasciculus and the fronto-parietal connections (anterior segment) of the arcuate fasciculus. Furthermore, males showed a left lateralization of the fronto-temporal segment of the arcuate fasciculus (long segment), while females had a more bilateral distribution. In two patients with brain lesions, DTI was acquired and tractography used to show that the tracts affected by the lesions were correctly identified by the atlas. This study suggests that DTI-derived maps can be used together with a previous histological atlas to establish the relationship of focal lesions with nearby tracts and improve clinico-anatomical correlation.

  13. Quantitative map of multiple auditory cortical regions with a stereotaxic fine-scale atlas of the mouse brain

    PubMed Central

    Tsukano, Hiroaki; Horie, Masao; Hishida, Ryuichi; Takahashi, Kuniyuki; Takebayashi, Hirohide; Shibuki, Katsuei

    2016-01-01

    Optical imaging studies have recently revealed the presence of multiple auditory cortical regions in the mouse brain. We have previously demonstrated, using flavoprotein fluorescence imaging, at least six regions in the mouse auditory cortex, including the anterior auditory field (AAF), primary auditory cortex (AI), the secondary auditory field (AII), dorsoanterior field (DA), dorsomedial field (DM), and dorsoposterior field (DP). While multiple regions in the visual cortex and somatosensory cortex have been annotated and consolidated in recent brain atlases, the multiple auditory cortical regions have not yet been presented from a coronal view. In the current study, we obtained regional coordinates of the six auditory cortical regions of the C57BL/6 mouse brain and illustrated these regions on template coronal brain slices. These results should reinforce the existing mouse brain atlases and support future studies in the auditory cortex. PMID:26924462

  14. Automatic brain segmentation and validation: image-based versus atlas-based deformable models

    NASA Astrophysics Data System (ADS)

    Aboutanos, Georges B.; Dawant, Benoit M.

    1997-04-01

    Due to the complexity of the brain surface, there is at present no segmentation method that proves to work automatically and consistently on any 3-D magnetic resonance (MR) images of the head. There is a definite lack of validation studies related to automatic brain extraction. In this work we present an image-base automatic method for brain segmentation and use its results as an input to a deformable model method which we call image-based deformable model. Combining image-based methods with a deformable model can lead to a robust segmentation method without requiring registration of the image volumes into a standardized space, the automation of which remains challenging for pathological cases. We validate our segmentation results on 3-D MP-RAGE (magnetization-prepared rapid gradient-echo) volumes for the image model prior- and post-deformation and compare it to an atlas model prior- and post-deformation. Our validation is based on volume measurement comparison to manually segmented data. Our analysis shows that the improvement afforded by the deformable model methods are statistically significant, however there are no significant differences between the image-based and atlas-based deformable model methods.

  15. A digital interactive human brain atlas based on Chinese visible human datasets for anatomy teaching.

    PubMed

    Li, Qiyu; Ran, Xu; Zhang, Shaoxiang; Tan, Liwen; Qiu, Mingguo

    2014-01-01

    As we know, the human brain is one of the most complicated organs in the human body, which is the key and difficult point in neuroanatomy and sectional anatomy teaching. With the rapid development and extensive application of imaging technology in clinical diagnosis, doctors are facing higher and higher requirement on their anatomy knowledge. Thus, to cultivate medical students to meet the needs of medical development today and to improve their ability to read and understand radiographic images have become urgent challenges for the medical teachers. In this context, we developed a digital interactive human brain atlas based on the Chinese visible human datasets for anatomy teaching (available for free download from http://www.chinesevisiblehuman.com/down/DHBA.rar). The atlas simultaneously provides views in all 3 primary planes of section. The main structures of the human brain have been anatomically labeled in all 3 views. It is potentially useful for anatomy browsing, user self-testing, and automatic student assessment. In a word, it is interactive, 3D, user friendly, and free of charge, which can provide a new, intuitive means for anatomy teaching.

  16. Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR.

    PubMed

    Merida, Ines; Reilhac, Anthonin; Redoute, Jerome; Heckemann, Rolf; Costes, Nicolas; Hammers, Alexander

    2017-02-09

    Introduction In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. Methods A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). Results On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the

  17. Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR

    NASA Astrophysics Data System (ADS)

    Mérida, Inés; Reilhac, Anthonin; Redouté, Jérôme; Heckemann, Rolf A.; Costes, Nicolas; Hammers, Alexander

    2017-04-01

    In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to  +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the attenuation maps. This

  18. Recent Science Highlights of the Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Ukhorskiy, Aleksandr

    2016-10-01

    The morning of 30 August 2012 saw an Atlas 5 rocket launch NASA's second Living With a Star spacecraft mission, the twin Radiation Belt Storm Probes, into an elliptic orbit cutting through Earth's radiation belts. Renamed the Van Allen Probes soon after launch, the Probes are designed to determine how the highly variable populations of high-energy charged particles within the radiation belts, dangerous to astronauts and satellites, are created, respond to solar variations, and evolve in space environments. The Van Allen Probes mission extends beyond the practical considerations of the hazard's of Earth's space environment. Twentieth century observations of space and astrophysical systems throughout the solar system and out into the observable universe have shown that the processes that generate intense particle radiation within magnetized environments such as Earth's are universal. During its mission the Van Allen Probes verified and quantified previously suggested energization processes, discovered new energization mechanisms, revealed the critical importance of dynamic plasma injections into the innermost magnetosphere, and used uniquely capable instruments to reveal inner radiation belt features that were all but invisible to previous sensors. This paper gives a brief overview of the mission, presents some recent science highlights, and discusses plans for the extended mission.

  19. A human brain atlas derived via n-cut parcellation of resting-state and task-based fMRI data.

    PubMed

    James, George Andrew; Hazaroglu, Onder; Bush, Keith A

    2016-02-01

    The growth of functional MRI has led to development of human brain atlases derived by parcellating resting-state connectivity patterns into functionally independent regions of interest (ROIs). All functional atlases to date have been derived from resting-state fMRI data. But given that functional connectivity between regions varies with task, we hypothesized that an atlas incorporating both resting-state and task-based fMRI data would produce an atlas with finer characterization of task-relevant regions than an atlas derived from resting-state alone. To test this hypothesis, we derived parcellation atlases from twenty-nine healthy adult participants enrolled in the Cognitive Connectome project, an initiative to improve functional MRI's translation into clinical decision-making by mapping normative variance in brain-behavior relationships. Participants underwent resting-state and task-based fMRI spanning nine cognitive domains: motor, visuospatial, attention, language, memory, affective processing, decision-making, working memory, and executive function. Spatially constrained n-cut parcellation derived brain atlases using (1) all participants' functional data (Task) or (2) a single resting-state scan (Rest). An atlas was also derived from random parcellation for comparison purposes (Random). Two methods were compared: (1) a parcellation applied to the group's mean edge weights (mean), and (2) a two-stage approach with parcellation of individual edge weights followed by parcellation of mean binarized edges (two-stage). The resulting Task and Rest atlases had significantly greater similarity with each other (mean Jaccard indices JI=0.72-0.85) than with the Random atlases (JI=0.59-0.63; all p<0.001 after Bonferroni correction). Task and Rest atlas similarity was greatest for the two-stage method (JI=0.85), which has been shown as more robust than the mean method; these atlases also better reproduced voxelwise seed maps of the left dorsolateral prefrontal cortex during

  20. Connecting Imaging Mass Spectrometry and Magnetic Resonance Imaging-based Anatomical Atlases for Automated Anatomical Interpretation and Differential Analysis.

    PubMed

    Verbeeck, Nico; Spraggins, Jeffrey M; Murphy, Monika J M; Wang, Hui-Dong; Deutch, Ariel Y; Caprioli, Richard M; de Plas, Raf Van

    2017-02-27

    Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model, which are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities.

  1. A Critique of Mark D. Allen's "The Preservation of Verb Subcategory Knowledge in a Spoken Language Comprehension Deficit"

    ERIC Educational Resources Information Center

    Kemmerer, David

    2008-01-01

    Allen [Allen, M. (2005). "The preservation of verb subcategory knowledge in a spoken language comprehension deficit." "Brain and Language, 95", 255-264.] reports a single patient, WBN, who, during spoken language comprehension, is still able to access some of the syntactic properties of verbs despite being unable to access some of their semantic…

  2. The Brain Analysis Library of Spatial maps and Atlases (BALSA) database.

    PubMed

    Van Essen, David C; Smith, John; Glasser, Matthew F; Elam, Jennifer; Donahue, Chad J; Dierker, Donna L; Reid, Erin K; Coalson, Timothy; Harwell, John

    2017-01-01

    We report on a new neuroimaging database, BALSA, that is a repository for extensively analyzed neuroimaging datasets from humans and nonhuman primates. BALSA is organized into two distinct sections. BALSA Reference is a curated repository of reference data accurately mapped to brain atlas surfaces and volumes, including various types of anatomically and functionally derived spatial maps as well as brain connectivity. BALSA Studies is a repository of extensively analyzed neuroimaging and neuroanatomical datasets associated with specific published studies, as voluntarily submitted by authors. It is particularly well suited for sharing of neuroimaging data as displayed in published figures. Uploading and downloading of data to BALSA involves 'scene' files that replicate how datasets appear in Connectome Workbench visualization software. Altogether, BALSA offers efficient access to richly informative datasets that are related to but transcend the images available in scientific publications.

  3. Optimizing the delivery of deep brain stimulation using electrophysiological atlases and an inverse modeling approach

    NASA Astrophysics Data System (ADS)

    Sun, Kay; Pallavaram, Srivatsan; Rodriguez, William; D'Haese, Pierre-Francois; Dawant, Benoit M.; Miga, Michael I.

    2012-02-01

    The use of deep brain stimulation (DBS) for the treatment of neurological movement degenerative disorders requires the precise placement of the stimulating electrode and the determination of optimal stimulation parameters that maximize symptom relief (e.g. tremor, rigidity, movement difficulties, etc.) while minimizing undesired physiological side-effects. This study demonstrates the feasibility of determining the ideal electrode placement and stimulation current amplitude by performing a patient-specific multivariate optimization using electrophysiological atlases and a bioelectric finite element model of the brain. Using one clinical case as a preliminary test, the optimization routine is able to find the most efficacious electrode location while avoiding the high side-effect regions. Future work involves optimization validation clinically and improvement to the accuracy of the model.

  4. Automatic Testing and Assessment of Neuroanatomy Using a Digital Brain Atlas: Method and Development of Computer- and Mobile-Based Applications

    ERIC Educational Resources Information Center

    Nowinski, Wieslaw L.; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G.; Marchenko, Yevgen; Volkau, Ihar

    2009-01-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to "Terminologia…

  5. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    NASA Astrophysics Data System (ADS)

    Purger, David; McNutt, Todd; Achanta, Pragathi; Quiñones-Hinojosa, Alfredo; Wong, John; Ford, Eric

    2009-12-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment.

  6. Reaction of oxygen with allene

    SciTech Connect

    Huang, Sheng-yu

    1988-07-01

    Elastic scattering studies carried out independently of the work related to the title forms the first section of the dissertation. The low-energy elastic scattering of He with Ar, Kr, Xe has been studied by molecular beam techniques. Two potential forms, exponential-spline-Morse-Morse-spline-van de Waals (ESMMSV) and Simon-Parr-Finlan-Dunham (SPFD), have been used to fit the measured differential cross section. Elastic scattering theory and experimental details are introduced. The reactive scattering of O(/sup 3/P) with allene has been studied using crossed molecular beams. Differing from the well known central-carbon-attack (CCA) mechanism in which the final products, carbon monoxide and ethylene, are obtained via a ring intermediate, a new mechanism, terminal-carbon-attack (TCA), has been observed. The production of O(/sup 3/P) atoms by radio frequency discharge is also introduced. To assist understanding of the experiments a multi-configuration self-consistent field (MCSCF) study of the reaction of O(/sup 3/P) with allene has been carried out. The key feature of the oxygen-allene potential energy surface for both CCA and TCA channels has been calculated with single-zeta (SZ), double-zeta (DZ), and double-zeta plus polarization (DZP) basis sets. Finally, an algorithm for optimizing the trial wavefunction in quantum Monte Carlo calculations has been developed. With the application of group theory, a symmetry-constrained optimization process can yield an improved trial wavefunction for the calculation of excited electronic state energies as well as the ground-state energy. Several applications are discussed. 145 refs.

  7. A spatiotemporal atlas of MR intensity, tissue probability and shape of the fetal brain with application to segmentation

    PubMed Central

    Habas, Piotr A.; Kim, Kio; Corbett-Detig, James M.; Rousseau, Francois; Glenn, Orit A.; Barkovich, A. James; Studholme, Colin

    2010-01-01

    Modeling and analysis of MR images of the developing human brain is a challenge due to rapid changes in brain morphology and morphometry. We present an approach to the construction of a spatiotemporal atlas of the fetal brain with temporal models of MR intensity, tissue probability and shape changes. This spatiotemporal model is created from a set of reconstructed MR images of fetal subjects with different gestational ages. Groupwise registration of manual segmentations and voxelwise nonlinear modeling allow us to capture the appearance, disappearance and spatial variation of brain structures over time. Applying this model to atlas-based segmentation, we generate age-specific MR templates and tissue probability maps and use them to initialize automatic tissue delineation in new MR images. The choice of model parameters and the final performance are evaluated using clinical MR scans of young fetuses with gestational ages ranging from 20.57 to 24.71 weeks. Experimental results indicate that quadratic temporal models can correctly capture growth-related changes in the fetal brain anatomy and provide improvement in accuracy of atlas-based tissue segmentation. PMID:20600970

  8. Three-dimensional interactive and stereotactic human brain atlas of white matter tracts.

    PubMed

    Nowinski, Wieslaw L; Chua, Beng Choon; Yang, Guo Liang; Qian, Guo Yu

    2012-01-01

    We present a human brain atlas of white matter (WM) tracts containing 40 major tracts, which is three-dimensional (3D), segmented, labeled, interactive, stereotactic and correlated to structure and vasculature. We consider: (1) WM accuracy by correlating WM tracts to underlying neuroanatomy and quantifying them; (2) balance between realism and completeness by processing a sequence of track volumes generated for various parameters with the increasing track number to enable a tract "shape convergence". MPRAGE and DTI in 64 directions of the same subject were acquired on 3 Tesla. The method has three steps: DTI-MPRAGE registration, 3D tract generation from DTI, to WM reconstruction from MPRAGE to parcellation into 17 components. 82 track volumes were generated for a wide spectrum of parameter values: Fractional Anisotropy threshold in [0.0125, 0.55] and trajectory angle lower than 45°, 60°, 65°, 70°, 75°, 80°, 85°, 90°. For each tract, a sequence of track volumes was processed to create/edit contours delineating this tract to achieve its shape convergence. The parcellated tracts were grouped into commissures, associations, projections and posterior fossa tracts, and labeled following Terminologia Anatomica. To facilitate that, a dedicated tract editor is developed which processes multiple track volumes, handles tracts in three representations (tracks, contours, envelopes); provides editing/visualization simultaneously on axial, coronal, sagittal planes; enables tract labeling and coloring; and provides numerous tools (track counting, smoothing and length thresholding; representation conversion and saving; structural atlas support). A stereotactic tract atlas along with parcellated WM was developed to explore in real-time any individual tract or their groups along with surrounding neuroanatomy.

  9. Water resources of Allen Parish

    USGS Publications Warehouse

    Prakken, Lawrence B.; Griffith, Jason M.; Fendick, Robert B.

    2012-01-01

    In 2005, approximately 29.2 million gallons per day (Mgal/d) of water were withdrawn in Allen Parish, Louisiana, including about 26.8 Mgal/d from groundwater sources and 2.45 Mgal/d from surface-water sources. Rice irrigation accounted for 74 percent (21.7 Mgal/d) of the total water withdrawn. Other categories of use included public supply, industrial, rural domestic, livestock, general irrigation, and aquaculture. Water-use data collected at 5-year intervals from 1960 to 2005 indicate water withdrawals in the parish were greatest in 1960 (119 Mgal/d) and 1980 (98.7 Mgal/d). The substantial decrease in surface-water use between 1960 and 1965 is primarily attributable to rice-irrigation withdrawals declining from 61.2 to 6.74 Mgal/d. This fact sheet summarizes information on the water resources of Allen Parish, La. Information on groundwater and surface-water availability, quality, development, use, and trends is based on previously published reports listed in the Selected References section.

  10. A Pre-computed Brain Response Atlas for Instantaneous Strain Estimation in Contact Sports.

    PubMed

    Ji, Songbai; Zhao, Wei

    2015-08-01

    Finite element models of the human head play an important role in investigating the mechanisms of traumatic brain injury, including sports concussion. A critical limitation, however, is that they incur a substantial computational cost to simulate even a single impact. Therefore, current simulation schemes significantly hamper brain injury studies based on model-estimated tissue-level responses. In this study, we present a pre-computed brain response atlas (pcBRA) to substantially increase the simulation efficiency in estimating brain strains using isolated rotational acceleration impulses parameterized with four independent variables (peak magnitude and duration, and rotational axis azimuth and elevation angles) with values determined from on-field measurements. Using randomly generated testing datasets, the partially established pcBRA achieved a 100% success rate in interpolation based on element-wise differences in accumulated peak strain ([Formula: see text]) according to a "double-10%" criterion or average regional [Formula: see text] in generic regions and the corpus callosum. A similar performance was maintained in extrapolation. The pcBRA performance was further successfully validated against directly simulated responses from two independently measured typical real-world rotational profiles. The computational cost to estimate element-wise whole-brain or regional [Formula: see text] was 6 s and <0.01 s, respectively, vs. ~50 min directly simulating a 40 ms impulse. These findings suggest the pcBRA could substantially increase the throughput in impact simulation without significant loss of accuracy from the estimation itself and, thus, its potential to accelerate the exploration of the mechanisms of sports concussion in general. If successful, the pcBRA may also become a diagnostic adjunct in conjunction with sensors that measure head impact kinematics on the field to objectively monitor and identify tissue-level brain trauma in real-time for "return

  11. Atlas-based Segmentation of the Germinal Matrix from in Utero Clinical MRI of the Fetal Brain

    PubMed Central

    Kim, Kio; Rousseau, Francois; Glenn, Orit A.; Barkovich, A. James

    2012-01-01

    Recently developed techniques for reconstruction of high-resolution 3D images from fetal MR scans allows us to study the morphometry of developing brain tissues in utero. However, existing adult brain analysis methods cannot be directly applied as the anatomy of the fetal brain is significantly different in terms of geometry and tissue morphology. We describe an approach to atlas-based segmentation of the fetal brain with particular focus on the delineation of the germinal matrix, a transient structure related to brain growth. We segment 3D images reconstructed from in utero clinical MR scans and measure volumes of different brain tissue classes for a group of fetal subjects at gestational age 20.5–22.5 weeks. We also include a partial validation of the approach using manual tracing of the germinal matrix at different gestational ages. PMID:18979766

  12. Multi-region labeling and segmentation using a graph topology prior and atlas information in brain images.

    PubMed

    Al-Shaikhli, Saif Dawood Salman; Yang, Michael Ying; Rosenhahn, Bodo

    2014-12-01

    Medical image segmentation and anatomical structure labeling according to the types of the tissues are important for accurate diagnosis and therapy. In this paper, we propose a novel approach for multi-region labeling and segmentation, which is based on a topological graph prior and the topological information of an atlas, using a modified multi-level set energy minimization method in brain images. We consider a topological graph prior and atlas information to evolve the contour based on a topological relationship presented via a graph relation. This novel method is capable of segmenting adjacent objects with very close gray level in low resolution brain image that would be difficult to segment correctly using standard methods. The topological information of an atlas are transformed to the topological graph of a low resolution (noisy) brain image to obtain region labeling. We explain our algorithm and show the topological graph prior and label transformation techniques to explain how it gives precise multi-region segmentation and labeling. The proposed algorithm is capable of segmenting and labeling different regions in noisy or low resolution MRI brain images of different modalities. We compare our approaches with other state-of-the-art approaches for multi-region labeling and segmentation.

  13. The Brain of the Archerfish Toxotes chatareus: A Nissl-Based Neuroanatomical Atlas and Catecholaminergic/Cholinergic Systems

    PubMed Central

    Karoubi, Naomi; Segev, Ronen; Wullimann, Mario F.

    2016-01-01

    Over recent years, the seven-spot archerfish (Toxotes chatareus) has emerged as a new model for studies in visual and behavioral neuroscience thanks to its unique hunting strategy. Its natural ability to spit at insects outside of water can be used in the laboratory for well controlled behavioral experiments where the fish is trained to aim at targets on a screen. The need for a documentation of the neuroanatomy of this animal became critical as more research groups use it as a model. Here we present an atlas of adult T. chatareus specimens caught in the wild in South East Asia. The atlas shows representative sections of the brain and specific structures revealed by a classic Nissl staining as well as corresponding schematic drawings. Additional immunostainings for catecholaminergic and cholinergic systems were conducted to corroborate the identification of certain nuclei and the data of a whole brain scanner is available online. We describe the general features of the archerfish brain as well as its specificities, especially for the visual system and compare the neuroanatomy of the archerfish with other teleosts. This atlas of the archerfish brain shows all levels of the neuraxis and intends to provide a solid basis for further neuroscientific research on T. chatareus, in particular electrophysiological studies. PMID:27891081

  14. The Brain of the Archerfish Toxotes chatareus: A Nissl-Based Neuroanatomical Atlas and Catecholaminergic/Cholinergic Systems.

    PubMed

    Karoubi, Naomi; Segev, Ronen; Wullimann, Mario F

    2016-01-01

    Over recent years, the seven-spot archerfish (Toxotes chatareus) has emerged as a new model for studies in visual and behavioral neuroscience thanks to its unique hunting strategy. Its natural ability to spit at insects outside of water can be used in the laboratory for well controlled behavioral experiments where the fish is trained to aim at targets on a screen. The need for a documentation of the neuroanatomy of this animal became critical as more research groups use it as a model. Here we present an atlas of adult T. chatareus specimens caught in the wild in South East Asia. The atlas shows representative sections of the brain and specific structures revealed by a classic Nissl staining as well as corresponding schematic drawings. Additional immunostainings for catecholaminergic and cholinergic systems were conducted to corroborate the identification of certain nuclei and the data of a whole brain scanner is available online. We describe the general features of the archerfish brain as well as its specificities, especially for the visual system and compare the neuroanatomy of the archerfish with other teleosts. This atlas of the archerfish brain shows all levels of the neuraxis and intends to provide a solid basis for further neuroscientific research on T. chatareus, in particular electrophysiological studies.

  15. Evidence for potentials and limitations of brain plasticity using an atlas of functional resectability of WHO grade II gliomas: towards a "minimal common brain".

    PubMed

    Ius, Tamara; Angelini, Elsa; Thiebaut de Schotten, Michel; Mandonnet, Emmanuel; Duffau, Hugues

    2011-06-01

    Despite recent advances in non-invasive brain mapping imaging, the resectability of a given area in a patient harboring a WHO grade II glioma cannot be predicted preoperatively with high reliability, due to mechanisms of functional reorganization. Therefore, intraoperative mapping by direct electrical stimulation remains the gold standard for detection and preservation of eloquent areas during glioma surgery, because it enables to perform on-line anatomo-functional correlations. To study potentials and limitations of brain plasticity, we gathered 58 postoperative MRI of patients operated on for a WHO grade II glioma under direct electrical cortico-subcortical stimulation. Postoperative images were registered on the MNI template to construct an atlas of functional resectability for which each voxel represents the probability to observe residual non-resectable tumor, that is, non-compensable area. The resulting atlas offers a rigorous framework to identify areas with high plastic potential (i.e. with probabilities of residual tumor close to 0), with low compensatory capabilities (i.e. probabilities of residual tumor close to 1) and with intermediate level of resectability (probability around 0.5). The resulting atlas highlights the utmost importance of preserving a core of connectivity through the main associative pathways, namely, it supports the existence of a "minimal common brain" among patients.

  16. Statistical model of laminar structure for atlas-based segmentation of the fetal brain from in utero MR images

    NASA Astrophysics Data System (ADS)

    Habas, Piotr A.; Kim, Kio; Chandramohan, Dharshan; Rousseau, Francois; Glenn, Orit A.; Studholme, Colin

    2009-02-01

    Recent advances in MR and image analysis allow for reconstruction of high-resolution 3D images from clinical in utero scans of the human fetal brain. Automated segmentation of tissue types from MR images (MRI) is a key step in the quantitative analysis of brain development. Conventional atlas-based methods for adult brain segmentation are limited in their ability to accurately delineate complex structures of developing tissues from fetal MRI. In this paper, we formulate a novel geometric representation of the fetal brain aimed at capturing the laminar structure of developing anatomy. The proposed model uses a depth-based encoding of tissue occurrence within the fetal brain and provides an additional anatomical constraint in a form of a laminar prior that can be incorporated into conventional atlas-based EM segmentation. Validation experiments are performed using clinical in utero scans of 5 fetal subjects at gestational ages ranging from 20.5 to 22.5 weeks. Experimental results are evaluated against reference manual segmentations and quantified in terms of Dice similarity coefficient (DSC). The study demonstrates that the use of laminar depth-encoded tissue priors improves both the overall accuracy and precision of fetal brain segmentation. Particular refinement is observed in regions of the parietal and occipital lobes where the DSC index is improved from 0.81 to 0.82 for cortical grey matter, from 0.71 to 0.73 for the germinal matrix, and from 0.81 to 0.87 for white matter.

  17. Quantification of F-18 FDG PET images in temporal lobe epilepsy patients using probabilistic brain atlas.

    PubMed

    Kang, K W; Lee, D S; Cho, J H; Lee, J S; Yeo, J S; Lee, S K; Chung, J K; Lee, M C

    2001-07-01

    A probabilistic atlas of the human brain (Statistical Probabilistic Anatomical Maps: SPAM) was developed by the international consortium for brain mapping (ICBM). It is a good frame for calculating volume of interest (VOI) in many fields of brain images. After calculating the counts in VOI using the product of probability of SPAM images and counts in FDG images, asymmetric indices (AI) were calculated and used for finding epileptogenic zones in mesial temporal lobe epilepsy (mTLE). FDG PET images from 18 surgically confirmed mTLE patients and 22 age-matched controls were spatially normalized to the average brain MRI template of ICBM. Counts from normalized PET images were multiplied with the probability of 12 VOIs from SPAM images in both temporal lobes. Finally AI were calculated on each pair of VOIs, and compared with visual assessment. If AI of mTLE patients were not within 2.9 standard deviation from those of normal control group (P < 0.008; Bonferroni correction for P < 0.05), epileptogenic zones were considered to be found successfully. The counts of VOIs in the normal control group were symmetric (AI < 4.3%, paired t test P > 0.05) except for those of the inferior temporal gyrus (P < 0.001). By AIs in six pairs of VOIs, PET in mTLE had deficit on one side (P < 0.05). Lateralization was correct in only 14/18 of patients by AI, but 17/18 were consistent with visual inspection. In three patients with normal AI, PET images were symmetric on visual inspection. The asymmetric indices obtained by taking the product of the statistical probability anatomical map and FDG PET, correlated well with visual assessment in mTLE patients. SPAM is useful for the quantification of VOIs in functional images.

  18. Automated voxel classification used with atlas-guided diffuse optical tomography for assessment of functional brain networks in young and older adults.

    PubMed

    Li, Lin; Cazzell, Mary; Babawale, Olajide; Liu, Hanli

    2016-10-01

    Atlas-guided diffuse optical tomography (atlas-DOT) is a computational means to image changes in cortical hemodynamic signals during human brain activities. Graph theory analysis (GTA) is a network analysis tool commonly used in functional neuroimaging to study brain networks. Atlas-DOT has not been analyzed with GTA to derive large-scale brain connectivity/networks based on near-infrared spectroscopy (NIRS) measurements. We introduced an automated voxel classification (AVC) method that facilitated the use of GTA with atlas-DOT images by grouping unequal-sized finite element voxels into anatomically meaningful regions of interest within the human brain. The overall approach included volume segmentation, AVC, and cross-correlation. To demonstrate the usefulness of AVC, we applied reproducibility analysis to resting-state functional connectivity measurements conducted from 15 young adults in a two-week period. We also quantified and compared changes in several brain network metrics between young and older adults, which were in agreement with those reported by a previous positron emission tomography study. Overall, this study demonstrated that AVC is a useful means for facilitating integration or combination of atlas-DOT with GTA and thus for quantifying NIRS-based, voxel-wise resting-state functional brain networks.

  19. A mu-delta opioid receptor brain atlas reveals neuronal co-occurrence in subcortical networks.

    PubMed

    Erbs, Eric; Faget, Lauren; Scherrer, Gregory; Matifas, Audrey; Filliol, Dominique; Vonesch, Jean-Luc; Koch, Marc; Kessler, Pascal; Hentsch, Didier; Birling, Marie-Christine; Koutsourakis, Manoussos; Vasseur, Laurent; Veinante, Pierre; Kieffer, Brigitte L; Massotte, Dominique

    2015-03-01

    Opioid receptors are G protein-coupled receptors (GPCRs) that modulate brain function at all levels of neural integration, including autonomic, sensory, emotional and cognitive processing. Mu (MOR) and delta (DOR) opioid receptors functionally interact in vivo, but whether interactions occur at circuitry, cellular or molecular levels remains unsolved. To challenge the hypothesis of MOR/DOR heteromerization in the brain, we generated redMOR/greenDOR double knock-in mice and report dual receptor mapping throughout the nervous system. Data are organized as an interactive database offering an opioid receptor atlas with concomitant MOR/DOR visualization at subcellular resolution, accessible online. We also provide co-immunoprecipitation-based evidence for receptor heteromerization in these mice. In the forebrain, MOR and DOR are mainly detected in separate neurons, suggesting system-level interactions in high-order processing. In contrast, neuronal co-localization is detected in subcortical networks essential for survival involved in eating and sexual behaviors or perception and response to aversive stimuli. In addition, potential MOR/DOR intracellular interactions within the nociceptive pathway offer novel therapeutic perspectives.

  20. A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI.

    PubMed

    Schwarz, Adam J; Danckaert, Anne; Reese, Torsten; Gozzi, Alessandro; Paxinos, George; Watson, Charles; Merlo-Pich, Emilio V; Bifone, Angelo

    2006-08-15

    We describe a stereotaxic rat brain MRI template set with a co-registered digital anatomical atlas and illustrate its application to the analysis of a pharmacological MRI (phMRI) study of apomorphine. The template set includes anatomical images and tissue class probability maps for brain parenchyma and cerebrospinal fluid (CSF). These facilitate the use of standard fMRI software for spatial normalisation and tissue segmentation of rat brain data. A volumetric reconstruction of the Paxinos and Watson rat brain atlas is also co-localised with the template, enabling the atlas structure and stereotaxic coordinates corresponding to a feature within a statistical map to be interactively reported, facilitating the localisation of functional effects. Moreover, voxels falling within selected brain structures can be combined to define anatomically based 3D volumes of interest (VOIs), free of operator bias. As many atlas structures are small relative to the typical resolution of phMRI studies, a mechanism for defining composite structures as agglomerations of individual atlas structures is also described. This provides a simple and robust means of interrogating structures that are otherwise difficult to delineate and an objective framework for comparing and classifying compounds based on an anatomical profile of their activity. These developments allow a closer alignment of pre-clinical and clinical analysis techniques.

  1. Van Allen Discovery Most Important

    NASA Technical Reports Server (NTRS)

    Jastrow, R.

    1959-01-01

    The first step toward the exploration of space occurred approximately 22 months ago as a part of the International Geophysical Year. In the short interval since October, 1957, the new tools of research, the satellite and the space rocket, have produced two unexpected results of fundamental scientific importance. First, instruments placed in the Explorer satellites by James A. Van Allen have revealed the existence of layers of energetic particles in the outer atmosphere. This discovery constitutes the most significant research achievement of the IGY satellite program. The layers may provide the explanation for the aurora and other geophysical phenomena, and they will also influence the design of vehicles for manned space flight, whose occupants must be shielded against their harmful biological effects. Second, the shape of the earth has been determined very accurately with the aid of data from the first Vanguard. As a result of this investigation, we have found that our planet tends toward the shape of a pear, with its stem at the North Pole. This discovery may produce major changes in our ideas on the interior structure of the earth.

  2. Phosphine Catalysis of Allenes with Electrophiles

    PubMed Central

    Wang, Zhiming; Xu, Xingzhu; Kwon, Ohyun

    2014-01-01

    Nucleophilic phosphine catalysis of allenes with electrophiles is one of the most powerful and straightforward synthetic strategies for the generation of highly functionalized carbocycle or heterocycle structural motifs, which are present in a wide range of bioactive natural products and medicinally important substances. The reaction topologies can be controlled through judicious choice of the phosphine catalyst and the structural variations of starting materials. This Tutorial Review presents selected examples of nucleophilic phosphine catalysis using allenes and electrophiles. PMID:24663290

  3. Multiscale image and multiscale deformation of brain anatomy for building average brain atlases

    NASA Astrophysics Data System (ADS)

    Studholme, Colin; Cardenas, Valerie A.; Weiner, Michael W.

    2001-07-01

    In this work we consider the process of aligning a set of anatomical MRI scans, from a group of subjects, to a single reference MRI scan as accurately as possible. A key requirement of this anatomical normalization is the ability to bring into alignment brain images with different ages and disease states with equal accuracy and precision, enabling the unbiased comparison of different groups. Typical images of such anatomy may vary in terms of both tissue shape, location and contrast. To address this we have developed, a highly localized free-form inter-subject registration algorithm driven by normalized mutual information. This employs an efficient multi-image resolution and multi-deformation resolution registration procedure. In this paper we examine the behavior of this algorithm when applied to aligning high-resolution MRI of groups of younger, older and atrophied brain anatomy to different target anatomies. To gain an insight into the quality of the spatial normalization, we have examined two properties of the transformations: The residual intensity differences between spatially normalized MRI values and the spatial discrepancies in transformation estimates between group and reference, derived from transformations between 168 different image pairs. These are examined with respect to the coarseness of the deformation model employed.

  4. Gene expression based mouse brain parcellation using Markov random field regularized non-negative matrix factorization

    NASA Astrophysics Data System (ADS)

    Pathak, Sayan D.; Haynor, David R.; Thompson, Carol L.; Lein, Ed; Hawrylycz, Michael

    2009-02-01

    Understanding the geography of genetic expression in the mouse brain has opened previously unexplored avenues in neuroinformatics. The Allen Brain Atlas (www.brain-map.org) (ABA) provides genome-wide colorimetric in situ hybridization (ISH) gene expression images at high spatial resolution, all mapped to a common three-dimensional 200μm3 spatial framework defined by the Allen Reference Atlas (ARA) and is a unique data set for studying expression based structural and functional organization of the brain. The goal of this study was to facilitate an unbiased data-driven structural partitioning of the major structures in the mouse brain. We have developed an algorithm that uses nonnegative matrix factorization (NMF) to perform parts based analysis of ISH gene expression images. The standard NMF approach and its variants are limited in their ability to flexibly integrate prior knowledge, in the context of spatial data. In this paper, we introduce spatial connectivity as an additional regularization in NMF decomposition via the use of Markov Random Fields (mNMF). The mNMF algorithm alternates neighborhood updates with iterations of the standard NMF algorithm to exploit spatial correlations in the data. We present the algorithm and show the sub-divisions of hippocampus and somatosensory-cortex obtained via this approach. The results are compared with established neuroanatomic knowledge. We also highlight novel gene expression based sub divisions of the hippocampus identified by using the mNMF algorithm.

  5. Generation and Disease Model Relevance of a Manganese Enhanced Magnetic Resonance Imaging-Based NOD/scid-IL-2Rγcnull Mouse Brain Atlas

    PubMed Central

    Sajja, Balasrinivasa R.; Bade, Aditya N.; Zhou, Biyun; Uberti, Mariano G.; Gorantla, Santhi; Gendelman, Howard E.; Boska, Michael D.; Liu, Yutong

    2016-01-01

    Strain specific mouse brain magnetic resonance imaging (MRI) atlases provide coordinate space linked anatomical registration. This allows longitudinal quantitative analyses of neuroanatomical volumes and imaging metrics for assessing the role played by aging and disease to the central nervous system. As NOD/scid-IL-2Rγcnull (NSG) mice allow human cell transplantation to study human disease, these animals are used to assess brain morphology. Manganese enhanced MRI (MEMRI) improves contrasts amongst brain components and as such can greatly help identifying a broad number of structures on MRI. To this end, NSG adult mouse brains were imaged in vivo on a 7.0 Tesla MR scanner at an isotropic resolution of 100 µm. A population averaged brain of 19 mice was generated using an iterative alignment algorithm. MEMRI provided sufficient contrast permitting 41 brain structures to be manually labeled. Volumes of 7 humanized mice brain structures were measured by atlas-based segmentation and compared against non-humanized controls. The humanized NSG mice brain volumes were smaller than controls (p<0.001). Many brain structures of humanized mice were significantly smaller than controls. We posit that the irradiation and cell grafting involved in the creation of humanized mice were responsible for the morphological differences. Six NSG mice without MnCl2 administration were scanned with high resolution T2-weighted MRI and segmented to test broad utility of the atlas. PMID:26556033

  6. Detection, visualization and animation of abnormal anatomic structure with a deformable probabilistic brain atlas based on random vector field transformations.

    PubMed

    Thompson, P M; Toga, A W

    1997-09-01

    This paper describes the design, implementation and preliminary results of a technique for creating a comprehensive probabilistic atlas of the human brain based on high-dimensional vector field transformations. The goal of the atlas is to detect and quantify distributed patterns of deviation from normal anatomy, in a 3-D brain image from any given subject. The algorithm analyzes a reference population of normal scans and automatically generates color-coded probability maps of the anatomy of new subjects. Given a 3-D brain image of a new subject, the algorithm calculates a set of high-dimensional volumetric maps (with typically 384(2) x 256 x 3 approximately 10(8) degrees of freedom) elastically deforming this scan into structural correspondence with other scans, selected one by one from an anatomic image database. The family of volumetric warps thus constructed encodes statistical properties and directional biases of local anatomical variation throughout the architecture of the brain. A probability space of random transformations, based on the theory of anisotropic Gaussian random fields, is then developed to reflect the observed variability in stereotaxic space of the points whose correspondences are found by the warping algorithm. A complete system of 384(2) x 256 probability density functions is computed, yielding confidence limits in stereotaxic space for the location of every point represented in the 3-D image lattice of the new subject's brain. Color-coded probability maps are generated, densely defined throughout the anatomy of the new subject. These indicate locally the probability of each anatomic point being unusually situated, given the distributions of corresponding points in the scans of normal subjects. 3-D MRI and high-resolution cryosection volumes are analyzed from subjects with metastatic tumors and Alzheimer's disease. Gradual variations and continuous deformations of the underlying anatomy are simulated and their dynamic effects on regional

  7. Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas

    PubMed Central

    Rojas, Gonzalo M.; Gálvez, Marcelo; Vega Potler, Natan; Craddock, R. Cameron; Margulies, Daniel S.; Castellanos, F. Xavier; Milham, Michael P.

    2014-01-01

    Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity. PMID:25414626

  8. Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas.

    PubMed

    Rojas, Gonzalo M; Gálvez, Marcelo; Vega Potler, Natan; Craddock, R Cameron; Margulies, Daniel S; Castellanos, F Xavier; Milham, Michael P

    2014-01-01

    Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity.

  9. Electrophilic addition and cyclization reactions of allenes.

    PubMed

    Ma, Shengming

    2009-10-20

    Modern organic synthesis depends on the development of highly selective methods for the efficient construction of potentially useful target molecules. A primary goal in our laboratory is the discovery of new reactions that convert readily available starting materials to complex products with complete control of regio- and stereoselectivity. Allenes are one underused moiety in organic synthesis, because these groups are often thought to be highly reactive. However, many compounds containing the allene group, including natural products and pharmaceuticals, are fairly stable. The chemistry of allenes has been shown to have significant potential in organic synthesis. Electrophilic additions to allenes have often been considered to be synthetically less attractive due to the lack of efficient control of the regio- and stereoselectivity. However, this Account describes electrophilic reactions of allenes with defined regio- and stereoselectivity developed in our laboratory. Many substituted allenes are readily available from propargylic alcohols. Our work has involved an exploration of the reactions of these allenes with many different electrophiles: the E- or Z-halo- or seleno-hydroxylations of allenyl sulfoxides, sulfones, phosphine oxides, carboxylates, sulfides or selenides, butenolides, and arenes, and the halo- or selenolactonization reactions of allenoic acids and allenoates. These reactions have produced a host of new compounds such as stereodefined allylic alcohols, ethers, amides, thiiranes, and lactones. In all these reactions, water acts as a reactant and plays an important role in determining the reaction pathway and the stereoselectivity. The differing electronic properties of the two C=C bonds in these allenes determine the regioselectivity of these reactions. Through mechanistic studies of chirality transfer, isolation and reactivity of cyclic intermediates, (18)O-labeling, and substituent effects, we discovered that the E-stereoselectivity of some

  10. Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

    NASA Astrophysics Data System (ADS)

    Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

    2016-03-01

    The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

  11. A critique of Mark D. Allen's "the preservation of verb subcategory knowledge in a spoken language comprehension deficit".

    PubMed

    Kemmerer, David

    2008-07-01

    Allen [Allen, M. (2005). The preservation of verb subcategory knowledge in a spoken language comprehension deficit. Brain and Language, 95, 255-264.] reports a single patient, WBN, who, during spoken language comprehension, is still able to access some of the syntactic properties of verbs despite being unable to access some of their semantic properties. Allen claims that these findings challenge linguistic theories which assume that much of the syntactic behavior of verbs can be predicted from their meanings. I argue, however, that this conclusion is not supported by the data for two reasons: first, Allen focuses on aspects of verb syntax that are not claimed to be influenced by verb semantics; and second, he ignores aspects of verb syntax that are claimed to be influenced by verb semantics.

  12. Allen Auditorium attic looking from southeast corner. Wine barrels with ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Allen Auditorium attic looking from southeast corner. Wine barrels with scrap used for counterweight material for lift up walls no longer in use - Sheldon Jackson College, Richard H. Allen Memorial Hall, Lincoln Street, Sitka, Sitka Borough, AK

  13. Individual 3D region-of-interest atlas of the human brain: knowledge-based class image analysis for extraction of anatomical objects

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Sabri, Osama; Buell, Udalrich

    2000-06-01

    After neural network-based classification of tissue types, the second step of atlas extraction is knowledge-based class image analysis to get anatomically meaningful objects. Basic algorithms are region growing, mathematical morphology operations, and template matching. A special algorithm was designed for each object. The class label of each voxel and the knowledge about the relative position of anatomical objects to each other and to the sagittal midplane of the brain can be utilized for object extraction. User interaction is only necessary to define starting, mid- and end planes for most object extractions and to determine the number of iterations for erosion and dilation operations. Extraction can be done for the following anatomical brain regions: cerebrum; cerebral hemispheres; cerebellum; brain stem; white matter (e.g., centrum semiovale); gray matter [cortex, frontal, parietal, occipital, temporal lobes, cingulum, insula, basal ganglia (nuclei caudati, putamen, thalami)]. For atlas- based quantification of functional data, anatomical objects can be convoluted with the point spread function of functional data to take into account the different resolutions of morphological and functional modalities. This method allows individual atlas extraction from MRI image data of a patient without the need of warping individual data to an anatomical or statistical MRI brain atlas.

  14. William G. Allen: On "Orators and Oratory."

    ERIC Educational Resources Information Center

    Calloway-Thomas, Carolyn

    1988-01-01

    William G. Allen was an African-American professor at Central College, McGrawville, New York. His lecture, "Orators and Oratory," delivered on June 22, 1852, is the earliest recorded study by an American Black on the ancient art of oratory. The text of the lecture is provided. (BJV)

  15. Test-retest assessment of cortical activation induced by repetitive transcranial magnetic stimulation with brain atlas-guided optical topography

    NASA Astrophysics Data System (ADS)

    Tian, Fenghua; Kozel, F. Andrew; Yennu, Amarnath; Croarkin, Paul E.; McClintock, Shawn M.; Mapes, Kimberly S.; Husain, Mustafa M.; Liu, Hanli

    2012-11-01

    Repetitive transcranial magnetic stimulation (rTMS) is a technology that stimulates neurons with rapidly changing magnetic pulses with demonstrated therapeutic applications for various neuropsychiatric disorders. Functional near-infrared spectroscopy (fNIRS) is a suitable tool to assess rTMS-evoked brain responses without interference from the magnetic or electric fields generated by the TMS coil. We have previously reported a channel-wise study of combined rTMS/fNIRS on the motor and prefrontal cortices, showing a robust decrease of oxygenated hemoglobin concentration (Δ[HbO2]) at the sites of 1-Hz rTMS and the contralateral brain regions. However, the reliability of this putative clinical tool is unknown. In this study, we develop a rapid optical topography approach to spatially characterize the rTMS-evoked hemodynamic responses on a standard brain atlas. A hemispherical approximation of the brain is employed to convert the three-dimensional topography on the complex brain surface to a two-dimensional topography in the spherical coordinate system. The test-retest reliability of the combined rTMS/fNIRS is assessed using repeated measurements performed two to three days apart. The results demonstrate that the Δ[HbO2] amplitudes have moderate-to-high reliability at the group level; and the spatial patterns of the topographic images have high reproducibility in size and a moderate degree of overlap at the individual level.

  16. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

    PubMed Central

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G.; Leergaard, Trygve B.; Kirlangic, Mehmet E.; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  17. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas.

    PubMed

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G; Leergaard, Trygve B; Kirlangic, Mehmet E; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  18. Automatic segmentation of short association bundles using a new multi-subject atlas of the left hemisphere fronto-parietal brain connections.

    PubMed

    Guevara, M; Seguel, D; Roman, C; Duclap, D; Lebois, A; Le Bihan; Mangin, J-F; Poupon, C; Guevara, P

    2015-08-01

    Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of the pathogenesis associated to it. In this work we developed a method for the automatic creation of a SWM bundle multi-subject atlas. The atlas generation method is based on a cortical parcellation for the extraction of fibers connecting two different gyri. Then, an intra-subject fiber clustering is applied, in order to divide each bundle into sub-bundles with similar shape. After that, a two-step inter-subject fiber clustering is used in order to find the correspondence between the sub-bundles across the subjects, fuse similar clusters and discard the outliers. The method was applied to 40 subjects of a high quality HARDI database, focused on the left hemisphere fronto-parietal and insula brain regions. We obtained an atlas composed of 44 bundles connecting 22 pair of ROIs. Then the atlas was used to automatically segment 39 new subjects from the database.

  19. H. Julian Allen with Blunt Body Theory

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  20. Relationships between gene expression and brain wiring in the adult rodent brain.

    PubMed

    French, Leon; Pavlidis, Paul

    2011-01-06

    We studied the global relationship between gene expression and neuroanatomical connectivity in the adult rodent brain. We utilized a large data set of the rat brain "connectome" from the Brain Architecture Management System (942 brain regions and over 5000 connections) and used statistical approaches to relate the data to the gene expression signatures of 17,530 genes in 142 anatomical regions from the Allen Brain Atlas. Our analysis shows that adult gene expression signatures have a statistically significant relationship to connectivity. In particular, brain regions that have similar expression profiles tend to have similar connectivity profiles, and this effect is not entirely attributable to spatial correlations. In addition, brain regions which are connected have more similar expression patterns. Using a simple optimization approach, we identified a set of genes most correlated with neuroanatomical connectivity, and find that this set is enriched for genes involved in neuronal development and axon guidance. A number of the genes have been implicated in neurodevelopmental disorders such as autistic spectrum disorder. Our results have the potential to shed light on the role of gene expression patterns in influencing neuronal activity and connectivity, with potential applications to our understanding of brain disorders. Supplementary data are available at http://www.chibi.ubc.ca/ABAMS.

  1. Automatic testing and assessment of neuroanatomy using a digital brain atlas: method and development of computer- and mobile-based applications.

    PubMed

    Nowinski, Wieslaw L; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G; Marchenko, Yevgen; Volkau, Ihar

    2009-10-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to Terminologia Anatomica. Because the cerebral models are fully segmented and labeled, our approach enables automatic and random atlas-derived generation of questions to test location and naming of cerebral structures. This is done in four steps: test individualization by the instructor, test taking by the students at their convenience, automatic student assessment by the application, and communication of the individual assessment to the instructor. A computer-based application with an interactive 3D atlas and a preliminary mobile-based application were developed to realize this approach. The application works in two test modes: instructor and student. In the instructor mode, the instructor customizes the test by setting the scope of testing and student performance criteria, which takes a few seconds. In the student mode, the student is tested and automatically assessed. Self-testing is also feasible at any time and pace. Our approach is automatic both with respect to test generation and student assessment. It is also objective, rapid, and customizable. We believe that this approach is novel from computer-based, mobile-based, and atlas-assisted standpoints.

  2. Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights.

    PubMed

    Acquaah-Mensah, George K; Taylor, Ronald C

    2016-07-15

    Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen Brain Atlas mouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networks were learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations in mouse whole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, and Syn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD.

  3. Multi-atlas multi-shape segmentation of fetal brain MRI for volumetric and morphometric analysis of ventriculomegaly.

    PubMed

    Gholipour, Ali; Akhondi-Asl, Alireza; Estroff, Judy A; Warfield, Simon K

    2012-04-15

    The recent development of motion robust super-resolution fetal brain MRI holds out the potential for dramatic new advances in volumetric and morphometric analysis. Volumetric analysis based on volumetric and morphometric biomarkers of the developing fetal brain must include segmentation. Automatic segmentation of fetal brain MRI is challenging, however, due to the highly variable size and shape of the developing brain; possible structural abnormalities; and the relatively poor resolution of fetal MRI scans. To overcome these limitations, we present a novel, constrained, multi-atlas, multi-shape automatic segmentation method that specifically addresses the challenge of segmenting multiple structures with similar intensity values in subjects with strong anatomic variability. Accordingly, we have applied this method to shape segmentation of normal, dilated, or fused lateral ventricles for quantitative analysis of ventriculomegaly (VM), which is a pivotal finding in the earliest stages of fetal brain development, and warrants further investigation. Utilizing these innovative techniques, we introduce novel volumetric and morphometric biomarkers of VM comparing these values to those that are generated by standard methods of VM analysis, i.e., by measuring the ventricular atrial diameter (AD) on manually selected sections of 2D ultrasound or 2D MRI. To this end, we studied 25 normal and abnormal fetuses in the gestation age (GA) range of 19 to 39 weeks (mean=28.26, stdev=6.56). This heterogeneous dataset was essentially used to 1) validate our segmentation method for normal and abnormal ventricles; and 2) show that the proposed biomarkers may provide improved detection of VM as compared to the AD measurement.

  4. Individual 3D region-of-interest atlas of the human brain: automatic training point extraction for neural-network-based classification of brain tissue types

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-04-01

    Individual region-of-interest atlas extraction consists of two main parts: T1-weighted MRI grayscale images are classified into brain tissues types (gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB), background (BG)), followed by class image analysis to define automatically meaningful ROIs (e.g., cerebellum, cerebral lobes, etc.). The purpose of this algorithm is the automatic detection of training points for neural network-based classification of brain tissue types. One transaxial slice of the patient data set is analyzed. Background separation is done by simple region growing. A random generator extracts spatially uniformly distributed training points of class BG from that region. For WM training point extraction (TPE), the homogeneity operator is the most important. The most homogeneous voxels define the region for WM TPE. They are extracted by analyzing the cumulative histogram of the homogeneity operator response. Assuming a Gaussian gray value distribution in WM, a random number is used as a probabilistic threshold for TPE. Similarly, non-white matter and non-background regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is an additional feature. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated.

  5. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  6. Allenes and computational chemistry: from bonding situations to reaction mechanisms.

    PubMed

    Soriano, Elena; Fernández, Israel

    2014-05-07

    The present review is focused on the application of computational/theoretical methods to the wide and rich chemistry of allenes. Special emphasis is made on the interplay and synergy between experimental and computational methodologies, rather than on recent developments in methods and algorithms. Therefore, this review covers the state-of-the-art applications of computational chemistry to understand and rationalize the bonding situation and vast reactivity of allenes. Thus, the contents of this review span from the most fundamental studies on the equilibrium structure and chirality of allenes to recent advances in the study of complex reaction mechanisms involving allene derivatives in organic and organometallic chemistry.

  7. Quantitative Evaluation of Atlas-based Attenuation Correction for Brain PET in an Integrated Time-of-Flight PET/MR Imaging System.

    PubMed

    Yang, Jaewon; Jian, Yiqiang; Jenkins, Nathaniel; Behr, Spencer C; Hope, Thomas A; Larson, Peder E Z; Vigneron, Daniel; Seo, Youngho

    2017-02-23

    Purpose To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain positron emission tomography (PET) in an integrated time-of-flight (TOF) PET/magnetic resonance (MR) imaging system. Materials and Methods Thirty recruited patients provided informed consent in this institutional review board-approved study. All patients underwent whole-body fluorodeoxyglucose PET/computed tomography (CT) followed by TOF PET/MR imaging. With use of TOF PET data, PET images were reconstructed with four different attenuation correction (AC) methods: PET with patient CT-based AC (CTAC), PET with ATAC (air and bone from an atlas), PET with ATACpatientBone (air and tissue from the atlas with patient bone), and PET with ATACboneless (air and tissue from the atlas without bone). For quantitative evaluation, PET mean activity concentration values were measured in 14 1-mL volumes of interest (VOIs) distributed throughout the brain and statistical significance was tested with a paired t test. Results The mean overall difference (±standard deviation) of PET with ATAC compared with PET with CTAC was -0.69 kBq/mL ± 0.60 (-4.0% ± 3.2) (P < .001). The results were patient dependent (range, -9.3% to 0.57%) and VOI dependent (range, -5.9 to -2.2). In addition, when bone was not included for AC, the overall difference of PET with ATACboneless (-9.4% ± 3.7) was significantly worse than that of PET with ATAC (-4.0% ± 3.2) (P < .001). Finally, when patient bone was used for AC instead of atlas bone, the overall difference of PET with ATACpatientBone (-1.5% ± 1.5) improved over that of PET with ATAC (-4.0% ± 3.2) (P < .001). Conclusion ATAC in PET/MR imaging achieves similar quantification accuracy to that from CTAC by means of atlas-based bone compensation. However, patient-specific anatomic differences from the atlas causes bone attenuation differences and misclassified sinuses, which result in patient-dependent performance variation of ATAC. (©) RSNA, 2017

  8. Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: Application to normal elderly and Alzheimer’s disease participants

    PubMed Central

    Oishi, Kenichi; Faria, Andreia; Jiang, Hangyi; Li, Xin; Akhter, Kazi; Zhang, Jiangyang; Hsu, John T.; Miller, Michael I.; van Zijl, Peter C.M.; Albert, Marilyn; Lyketsos, Constantine G.; Woods, Roger; Toga, Arthur W.; Pike, G. Bruce; Rosa-Neto, Pedro; Evans, Alan; Mazziotta, John; Mori, Susumu

    2010-01-01

    The purpose of this paper is to establish single-participant white matter atlases based on diffusion tensor imaging. As one of the applications of the atlas, automated brain segmentation was performed and the accuracy was measured using Large Deformation Diffeomorphic Metric Mapping (LDDMM). High-quality diffusion tensor imaging (DTI) data from a single-participant were B0-distortion-corrected and transformed to the ICBM-152 atlas or to Talairach coordinates. The deep white matter structures, which have been previously well documented and clearly identified by DTI, were manually segmented. The superficial white matter areas beneath the cortex were defined, based on a population-averaged white matter probability map. The white matter was parcellated into 176 regions based on the anatomical labeling in the ICBM-DTI-81 atlas. The automated parcellation was achieved by warping this parcellation map to normal controls and to Alzheimer’s disease patients with severe anatomical atrophy. The parcellation accuracy was measured by a kappa analysis between the automated and manual parcellation at 11 anatomical regions. The kappa values were 0.70 for both normal controls and patients while the inter-rater reproducibility was 0.81 (controls) and 0.82 (patients), suggesting “almost perfect” agreement. A power analysis suggested that the proposed method is suitable for detecting FA and size abnormalities of the white matter in clinical studies. PMID:19385016

  9. Large-scale extraction of brain connectivity from the neuroscientific literature

    PubMed Central

    Richardet, Renaud; Chappelier, Jean-Cédric; Telefont, Martin; Hill, Sean

    2015-01-01

    Motivation: In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for modern neuroinformatics is finding methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and the integration of such data into computational models. A key example of this is metascale brain connectivity, where results are not reported in a normalized repository. Instead, these experimental results are published in natural language, scattered among individual scientific publications. This lack of normalization and centralization hinders the large-scale integration of brain connectivity results. In this article, we present text-mining models to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience. The brain regions are identified with three different named entity recognizers (NERs) and then normalized against two atlases: the Allen Brain Atlas (ABA) and the atlas from the Brain Architecture Management System (BAMS). We then use three different extractors to assess inter-region connectivity. Results: NERs and connectivity extractors are evaluated against a manually annotated corpus. The complete in litero extraction models are also evaluated against in vivo connectivity data from ABA with an estimated precision of 78%. The resulting database contains over 4 million brain region mentions and over 100 000 (ABA) and 122 000 (BAMS) potential brain region connections. This database drastically accelerates connectivity literature review, by providing a centralized repository of connectivity data to neuroscientists. Availability and implementation: The resulting models are publicly available at github.com/BlueBrain/bluima. Contact: renaud.richardet@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25609795

  10. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  11. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  12. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  13. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  14. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  15. An integrative analysis of regional gene expression profiles in the human brain.

    PubMed

    Myers, Emma M; Bartlett, Christopher W; Machiraju, Raghu; Bohland, Jason W

    2015-02-01

    Studies of the brain's transcriptome have become prominent in recent years, resulting in an accumulation of datasets with somewhat distinct attributes. These datasets, which are often analyzed only in isolation, also are often collected with divergent goals, which are reflected in their sampling properties. While many researchers have been interested in sampling gene expression in one or a few brain areas in a large number of subjects, recent efforts from the Allen Institute for Brain Sciences and others have focused instead on dense neuroanatomical sampling, necessarily limiting the number of individual donor brains studied. The purpose of the present work is to develop methods that draw on the complementary strengths of these two types of datasets for study of the human brain, and to characterize the anatomical specificity of gene expression profiles and gene co-expression networks derived from human brains using different specific technologies. The approach is applied using two publicly accessible datasets: (1) the high anatomical resolution Allen Human Brain Atlas (AHBA, Hawrylycz et al., 2012) and (2) a relatively large sample size, but comparatively coarse neuroanatomical dataset described previously by Gibbs et al. (2010). We found a relatively high degree of correspondence in differentially expressed genes and regional gene expression profiles across the two datasets. Gene co-expression networks defined in individual brain regions were less congruent, but also showed modest anatomical specificity. Using gene modules derived from the Gibbs dataset and from curated gene lists, we demonstrated varying degrees of anatomical specificity based on two classes of methods, one focused on network modularity and the other focused on enrichment of expression levels. Two approaches to assessing the statistical significance of a gene set's modularity in a given brain region were studied, which provide complementary information about the anatomical specificity of a gene

  16. Allenes in Asymmetric Catalysis. Asymmetric Ring-Opening of Meso-Epoxides Catalyzed by Allene-Containing Phosphine Oxides

    PubMed Central

    Pu, Xiaotao; Qi, Xiangbing; Ready, Joseph M.

    2009-01-01

    Unsymmetrically substituted allenes (1,2 dienes) are inherently chiral and can be prepared in optically pure form. Nonetheless, to date the allene framework has not been incorporated into ligands for asymmetric catalysis. Since allenes project functionality differently than either tetrahedral carbon or chiral biaryls, they may create complementary chiral environments. This study demonstrates that optically active C2 symmetric allene-containing bisphosphine oxides can catalyze the addition of SiCl4 to meso epoxides with high enantioselectivity. The epoxide-opening likely involves generation of a Lewis acidic, cationic (bisphosphine oxide)SiCl3 complex. The fact that high asymmetric induction is observed suggests that allenes may represent a new platform for the development of ligands and catalysts for asymmetric synthesis. PMID:19722613

  17. Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain

    PubMed Central

    Montoya, Julio Cesar; Fajardo, Dianora; Peña, Angela; Sánchez, Adalberto; Domínguez, Martha C; Satizábal, José María

    2014-01-01

    Background: The information of gene expression obtained from databases, have made possible the extraction and analysis of data related with several molecular processes involving not only in brain homeostasis but its disruption in some neuropathologies; principally in Down syndrome and the Alzheimer disease. Objective: To correlate the levels of transcription of 19 genes located in the Down Syndrome Critical Region (DSCR) with their expression in several substructures of normal human brain. Methods: There were obtained expression profiles of 19 DSCR genes in 42 brain substructures, from gene expression values available at the database of the human brain of the Brain Atlas of the Allen Institute for Brain Sciences", (http://human.brain-map.org/). The co-expression patterns of DSCR genes in brain were calculated by using multivariate statistical methods. Results: Highest levels of gene expression were registered at caudate nucleus, nucleus accumbens and putamen among central areas of cerebral cortex. Increased expression levels of RCAN1 that encode by a protein involved in signal transduction process of the CNS were recorded for PCP4 that participates in the binding to calmodulin and TTC3; a protein that is associated with differentiation of neurons. That previously identified brain structures play a crucial role in the learning process, in different class of memory and in motor skills. Conclusion: The precise regulation of DSCR gene expression is crucial to maintain the brain homeostasis, especially in those areas with high levels of gene expression associated with a remarkable process of learning and cognition. PMID:25767303

  18. A cross validation study of deep brain stimulation targeting: from experts to atlas-based, segmentation-based and automatic registration algorithms.

    PubMed

    Castro, F Javier Sanchez; Pollo, Claudio; Meuli, Reto; Maeder, Philippe; Cuisenaire, Olivier; Cuadra, Meritxell Bach; Villemure, Jean-Guy; Thiran, Jean-Philippe

    2006-11-01

    Validation of image registration algorithms is a difficult task and open-ended problem, usually application-dependent. In this paper, we focus on deep brain stimulation (DBS) targeting for the treatment of movement disorders like Parkinson's disease and essential tremor. DBS involves implantation of an electrode deep inside the brain to electrically stimulate specific areas shutting down the disease's symptoms. The subthalamic nucleus (STN) has turned out to be the optimal target for this kind of surgery. Unfortunately, the STN is in general not clearly distinguishable in common medical imaging modalities. Usual techniques to infer its location are the use of anatomical atlases and visible surrounding landmarks. Surgeons have to adjust the electrode intraoperatively using electrophysiological recordings and macrostimulation tests. We constructed a ground truth derived from specific patients whose STNs are clearly visible on magnetic resonance (MR) T2-weighted images. A patient is chosen as atlas both for the right and left sides. Then, by registering each patient with the atlas using different methods, several estimations of the STN location are obtained. Two studies are driven using our proposed validation scheme. First, a comparison between different atlas-based and nonrigid registration algorithms with a evaluation of their performance and usability to locate the STN automatically. Second, a study of which visible surrounding structures influence the STN location. The two studies are cross validated between them and against expert's variability. Using this scheme, we evaluated the expert's ability against the estimation error provided by the tested algorithms and we demonstrated that automatic STN targeting is possible and as accurate as the expert-driven techniques currently used. We also show which structures have to be taken into account to accurately estimate the STN location.

  19. NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain

    PubMed Central

    Gorgolewski, Krzysztof J.; Varoquaux, Gael; Rivera, Gabriel; Schwartz, Yannick; Sochat, Vanessa V.; Ghosh, Satrajit S.; Maumet, Camille; Nichols, Thomas E.; Poline, Jean-Baptiste; Yarkoni, Tal; Margulies, Daniel S.; Poldrack, Russell A.

    2016-01-01

    NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard, and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps. PMID:25869863

  20. Quantitative study on the hygroscopic expansion of spurr resin to obtain a high-resolution atlas of the mouse brain.

    PubMed

    Wang, Qingdi; Li, Anan; Gong, Hui; Xu, Dongli; Luo, Qingming

    2012-10-01

    Ultra-thin section-based microscopic imaging is considered one of the most realistic techniques for determining fine architectures of a brain-wide neural network. In this kind of method, the sample is usually embedded in resin and then immersed in water for sectioning and imaging. The effect of resin hygroscopic expansion on data accuracy and integrity is important as it may lead to inconsistent image qualities or degeneration of sectioning properties. But few studies have been conducted on this issue. Here, we have used surface profile measurements combined with sectioning and imaging by micro-optical sectioning tomography (MOST) to quantitatively study the sectioned surface expansion of spurr resin blocks as a result of water immersion for a short time period. The expansion effect on MOST imaging is also presented. The results revealed significant differences in the surface expansion of pure resin blocks with different immersion time durations (P < 0.001). During an eight-minute immersion, the surface expansion of the experimental specimens exhibited an approximately linear increase with immersion duration, while MOST images suffered a correlated decrease in brightness. Expansion was restricted to the submicron level with immersion duration of four minutes or less, and the mean and standard deviation of the expansion measurements both reached a maximum at eight minutes. When the immersion duration exceeded eight minutes, the expansion value decreased, which was most likely related to the degeneration of mechanical properties of the resin material on the block surface. This study indicates that it is necessary to select a specific sectioning mode according to the hygroscopic expansion properties of resin materials for maintaining the accuracy and integrity of whole brain atlas data.

  1. Automated anatomical interpretation of ion distributions in tissue: linking imaging mass spectrometry to curated atlases.

    PubMed

    Verbeeck, Nico; Yang, Junhai; De Moor, Bart; Caprioli, Richard M; Waelkens, Etienne; Van de Plas, Raf

    2014-09-16

    Imaging mass spectrometry (IMS) has become a prime tool for studying the distribution of biomolecules in tissue. Although IMS data sets can become very large, computational methods have made it practically feasible to search these experiments for relevant findings. However, these methods lack access to an important source of information that many human interpretations rely upon: anatomical insight. In this work, we address this need by (1) integrating a curated anatomical data source with an empirically acquired IMS data source, establishing an algorithm-accessible link between them and (2) demonstrating the potential of such an IMS-anatomical atlas link by applying it toward automated anatomical interpretation of ion distributions in tissue. The concept is demonstrated in mouse brain tissue, using the Allen Mouse Brain Atlas as the curated anatomical data source that is linked to MALDI-based IMS experiments. We first develop a method to spatially map the anatomical atlas to the IMS data sets using nonrigid registration techniques. Once a mapping is established, a second computational method, called correlation-based querying, gives an elementary demonstration of the link by delivering basic insight into relationships between ion images and anatomical structures. Finally, a third algorithm moves further beyond both registration and correlation by providing automated anatomical interpretation of ion images. This task is approached as an optimization problem that deconstructs ion distributions as combinations of known anatomical structures. We demonstrate that establishing a link between an IMS experiment and an anatomical atlas enables automated anatomical annotation, which can serve as an important accelerator both for human and machine-guided exploration of IMS experiments.

  2. Automated Anatomical Interpretation of Ion Distributions in Tissue: Linking Imaging Mass Spectrometry to Curated Atlases

    PubMed Central

    2015-01-01

    Imaging mass spectrometry (IMS) has become a prime tool for studying the distribution of biomolecules in tissue. Although IMS data sets can become very large, computational methods have made it practically feasible to search these experiments for relevant findings. However, these methods lack access to an important source of information that many human interpretations rely upon: anatomical insight. In this work, we address this need by (1) integrating a curated anatomical data source with an empirically acquired IMS data source, establishing an algorithm-accessible link between them and (2) demonstrating the potential of such an IMS-anatomical atlas link by applying it toward automated anatomical interpretation of ion distributions in tissue. The concept is demonstrated in mouse brain tissue, using the Allen Mouse Brain Atlas as the curated anatomical data source that is linked to MALDI-based IMS experiments. We first develop a method to spatially map the anatomical atlas to the IMS data sets using nonrigid registration techniques. Once a mapping is established, a second computational method, called correlation-based querying, gives an elementary demonstration of the link by delivering basic insight into relationships between ion images and anatomical structures. Finally, a third algorithm moves further beyond both registration and correlation by providing automated anatomical interpretation of ion images. This task is approached as an optimization problem that deconstructs ion distributions as combinations of known anatomical structures. We demonstrate that establishing a link between an IMS experiment and an anatomical atlas enables automated anatomical annotation, which can serve as an important accelerator both for human and machine-guided exploration of IMS experiments. PMID:25153352

  3. Brain-Derived Neurotrophic Factor and Antidepressive Effect of Electroconvulsive Therapy: Systematic Review and Meta-Analyses of the Preclinical and Clinical Literature

    PubMed Central

    Polyakova, M.; Schroeter, M. L.; Elzinga, B. M.; Holiga, S.; Schoenknecht, P.; de Kloet, E. R.; Molendijk, M. L.

    2015-01-01

    Emerging data suggest that Electro-Convulsive Treatment (ECT) may reduce depressive symptoms by increasing the expression of Brain-Derived Neurotrophic Factor (BDNF). Yet, conflicting findings have been reported. For this reason we performed a systematic review and meta-analysis of the preclinical and clinical literature on the association between ECT treatment (ECS in animals) and changes in BDNF concentrations and their effect on behavior. In addition, regional brain expression of BDNF in mouse and human brains were compared using Allen Brain Atlas. ECS, over sham, increased BDNF mRNA and protein in animal brain (effect size [Hedge’s g]: 0.38―0.54; 258 effect-size estimates, N = 4,284) but not in serum (g = 0.06, 95% CI = -0.05―0.17). In humans, plasma but not serum BDNF increased following ECT (g = 0.72 vs. g = 0.14; 23 effect sizes, n = 281). The gradient of the BDNF increment in animal brains corresponded to the gradient of the BDNF gene expression according to the Allen brain atlas. Effect-size estimates were larger following more ECT sessions in animals (r = 0.37, P < .0001) and in humans (r = 0.55; P = 0.05). There were some indications that the increase in BDNF expression was associated with behavioral changes in rodents, but not in humans. We conclude that ECS in rodents and ECT in humans increase BDNF concentrations but this is not consistently associated with changes in behavior. PMID:26529101

  4. Whole-brain mapping of behaviourally induced neural activation in mice.

    PubMed

    Vousden, Dulcie A; Epp, Jonathan; Okuno, Hiroyuki; Nieman, Brian J; van Eede, Matthijs; Dazai, Jun; Ragan, Timothy; Bito, Haruhiko; Frankland, Paul W; Lerch, Jason P; Henkelman, R Mark

    2015-07-01

    The ability to visualize behaviourally evoked neural activity patterns across the rodent brain is essential for understanding the distributed brain networks mediating particular behaviours. However, current imaging methods are limited in their spatial resolution and/or ability to obtain brain-wide coverage of functional activity. Here, we describe a new automated method for obtaining cellular-level, whole-brain maps of behaviourally induced neural activity in the mouse. This method combines the use of transgenic immediate-early gene reporter mice to visualize neural activity; serial two-photon tomography to image the entire brain at cellular resolution; advanced image processing algorithms to count the activated neurons and align the datasets to the Allen Mouse Brain Atlas; and statistical analysis to identify the network of activated brain regions evoked by behaviour. We demonstrate the use of this approach to determine the whole-brain networks activated during the retrieval of fear memories. Consistent with previous studies, we identified a large network of amygdalar, hippocampal, and neocortical brain regions implicated in fear memory retrieval. Our proposed methods can thus be used to map cellular networks involved in the expression of normal behaviours as well as to investigate in depth circuit dysfunction in mouse models of neurobiological disease.

  5. Expression Profiling of the Solute Carrier Gene Family in the Mouse BrainS⃞

    PubMed Central

    Dahlin, Amber; Royall, Josh; Hohmann, John G.; Wang, Joanne

    2009-01-01

    The solute carrier (Slc) superfamily is a major group of membrane transport proteins present in mammalian cells. Although Slc transporters play essential and diverse roles in the central nervous system, the localization and function of the vast majority of Slc genes in the mammalian brain are largely unknown. Using high-throughput in situ hybridization data generated by the Allen Brain Atlas, we systematically and quantitatively analyzed the spatial and cellular distribution of 307 Slc genes, which represent nearly 90% of presently known mouse Slc genes, in the adult C57BL/6J mouse brain. Our analysis showed that 252 (82%) of the 307 Slc genes are present in the brain, and a large proportion of these genes were detected at low to moderate expression levels. Evaluation of 20 anatomical brain subdivisions demonstrated a comparable level of Slc gene complexity but significant difference in transcript enrichment. The distribution of the expressed Slc genes was diverse, ranging from near-ubiquitous to highly localized. Functional annotation in 20 brain regions, including the blood-brain and blood-cerebral spinal fluid (CSF) barriers, suggests major roles of Slc transporters in supporting brain energy utilization, neurotransmission, nutrient supply, and CSF production. Furthermore, hierarchical cluster analysis revealed intricate Slc expression patterns associated with neuroanatomical organization. Our studies also revealed Slc genes present within defined brain microstructures and described the putative cell types expressing individual Slc genes. These results provide a useful resource for investigators to explore the roles of Slc genes in neurophysiological and pathological processes. PMID:19179540

  6. Population-averaged standard template brain atlas for the common marmoset (Callithrix jacchus).

    PubMed

    Hikishima, K; Quallo, M M; Komaki, Y; Yamada, M; Kawai, K; Momoshima, S; Okano, H J; Sasaki, E; Tamaoki, N; Lemon, R N; Iriki, A; Okano, H

    2011-02-14

    Advanced magnetic resonance (MR) neuroimaging analysis techniques based on voxel-wise statistics, such as voxel-based morphometry (VBM) and functional MRI, are widely applied to cognitive brain research in both human subjects and in non-human primates. Recent developments in imaging have enabled the evaluation of smaller animal models with sufficient spatial resolution. The common marmoset (Callithrix jacchus), a small New World primate species, has been widely used in neuroscience research, to which voxel-wise statistics could be extended with a species-specific brain template. Here, we report, for the first time, a tissue-segmented, population-averaged standard template of the common marmoset brain. This template was created by using anatomical T(1)-weighted images from 22 adult marmosets with a high-resolution isotropic voxel size of (0.2 mm)(3) at 7-Tesla and DARTEL algorithm in SPM8. Whole brain templates are available at International Neuroinformatics Japan Node website, http://brainatlas.brain.riken.jp/marmoset/.

  7. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation.

    PubMed

    Viader, Andreu; Ogasawara, Daisuke; Joslyn, Christopher M; Sanchez-Alavez, Manuel; Mori, Simone; Nguyen, William; Conti, Bruno; Cravatt, Benjamin F

    2016-01-18

    Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and -beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function.

  8. Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: EXTERIOR: WEST (CLARK STREET) AND SOUTH (JACKSON BLVD.) SIDES - U.S. Post Office, Customs House & Sub-Treasury, 218 South Dearborn Street, Chicago, Cook County, IL

  9. 8. Historic American Buildings Survey Harold Allen, Photographer 24 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Historic American Buildings Survey Harold Allen, Photographer 24 June 1964 GRAND STAIRWAY, FROM SECOND FLOOR HALL, SHOWING STAINED GLASS WINDOW IN WEST WALL ABOVE LANDING - Francis J. Dewes House, 503 West Wrightwood Avenue, Chicago, Cook County, IL

  10. 6. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Historic American Buildings Survey Harold Allen, Photographer June 1964 STAINED GLASS WINDOW, WEST WINDOW IN SOUTH WALL, FROM BALCONY - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  11. 1. Historic American Buildings Survey Harold Allen, Photographer 24 May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Historic American Buildings Survey Harold Allen, Photographer 24 May 1964 (R. TO L.) MANHATTAN BLDG. (WEST FRONT AND SOUTH SIDES), OLD COLONY BLDG., FISHER BLDG., MONADNOCK BLOCK - Manhattan Building, 431 South Dearborn Street, Chicago, Cook County, IL

  12. Substituent effects on dynamics at conical intersections: Allene and methyl allenes

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Wang, Yanmei; Boguslavskiy, Andrey E.; Stolow, Albert; Schuurman, Michael S.

    2016-01-01

    We report a joint experimental and theoretical study on the ultrafast excited state dynamics of allene and a series of its methylated analogues (1,2-butadiene, 1,1-dimethylallene, and tetramethylallene) in order to elucidate the conical intersection mediated dynamics that give rise to ultrafast relaxation to the ground electronic state. We use femtosecond time-resolved photoelectron spectroscopy (TRPES) to probe the coupled electronic-vibrational dynamics following UV excitation at 200 nm (6.2 eV). Ab initio multiple spawning (AIMS) simulations are employed to determine the mechanistic details of two competing dynamical pathways to the ground electronic state. In all molecules, these pathways are found to involve as follows: (i) twisting about the central allenic C-C-C axis followed by pyramidalization at one of the terminal carbon atoms and (ii) bending of allene moiety. Importantly, the AIMS trajectory data were used for ab initio simulations of the TRPES, permitting direct comparison with experiment. For each molecule, the decay of the TRPES signal is characterized by short (30 fs, 52 fs, 23 fs) and long (1.8 ps, 3.5 ps, [306 fs, 18 ps]) time constants for 1,2-butadiene, 1,1-dimethylallene, and tetramethylallene, respectively. However, AIMS simulations show that these time constants are only loosely related to the evolution of electronic character and actually more closely correlate to large amplitude motions on the electronic excited state, modulating the instantaneous vertical ionization potentials. Furthermore, the fully substituted tetramethylallene is observed to undergo qualitatively different dynamics, as displacements involving the relatively massive methyl groups impede direct access to the conical intersections which give rise to the ultrafast relaxation dynamics observed in the other species. These results show that the branching between the "twisting" and "bending" pathways can be modified via the selective methylation of the terminal carbon atoms of

  13. Substituent effects on dynamics at conical intersections: Allene and methyl allenes.

    PubMed

    Neville, Simon P; Wang, Yanmei; Boguslavskiy, Andrey E; Stolow, Albert; Schuurman, Michael S

    2016-01-07

    We report a joint experimental and theoretical study on the ultrafast excited state dynamics of allene and a series of its methylated analogues (1,2-butadiene, 1,1-dimethylallene, and tetramethylallene) in order to elucidate the conical intersection mediated dynamics that give rise to ultrafast relaxation to the ground electronic state. We use femtosecond time-resolved photoelectron spectroscopy (TRPES) to probe the coupled electronic-vibrational dynamics following UV excitation at 200 nm (6.2 eV). Ab initio multiple spawning (AIMS) simulations are employed to determine the mechanistic details of two competing dynamical pathways to the ground electronic state. In all molecules, these pathways are found to involve as follows: (i) twisting about the central allenic C-C-C axis followed by pyramidalization at one of the terminal carbon atoms and (ii) bending of allene moiety. Importantly, the AIMS trajectory data were used for ab initio simulations of the TRPES, permitting direct comparison with experiment. For each molecule, the decay of the TRPES signal is characterized by short (30 fs, 52 fs, 23 fs) and long (1.8 ps, 3.5 ps, [306 fs, 18 ps]) time constants for 1,2-butadiene, 1,1-dimethylallene, and tetramethylallene, respectively. However, AIMS simulations show that these time constants are only loosely related to the evolution of electronic character and actually more closely correlate to large amplitude motions on the electronic excited state, modulating the instantaneous vertical ionization potentials. Furthermore, the fully substituted tetramethylallene is observed to undergo qualitatively different dynamics, as displacements involving the relatively massive methyl groups impede direct access to the conical intersections which give rise to the ultrafast relaxation dynamics observed in the other species. These results show that the branching between the "twisting" and "bending" pathways can be modified via the selective methylation of the terminal carbon atoms of

  14. Substituent effects on dynamics at conical intersections: Allene and methyl allenes

    SciTech Connect

    Neville, Simon P.; Wang, Yanmei; Boguslavskiy, Andrey E.; Stolow, Albert; Schuurman, Michael S.

    2016-01-07

    We report a joint experimental and theoretical study on the ultrafast excited state dynamics of allene and a series of its methylated analogues (1,2-butadiene, 1,1-dimethylallene, and tetramethylallene) in order to elucidate the conical intersection mediated dynamics that give rise to ultrafast relaxation to the ground electronic state. We use femtosecond time-resolved photoelectron spectroscopy (TRPES) to probe the coupled electronic-vibrational dynamics following UV excitation at 200 nm (6.2 eV). Ab initio multiple spawning (AIMS) simulations are employed to determine the mechanistic details of two competing dynamical pathways to the ground electronic state. In all molecules, these pathways are found to involve as follows: (i) twisting about the central allenic C–C–C axis followed by pyramidalization at one of the terminal carbon atoms and (ii) bending of allene moiety. Importantly, the AIMS trajectory data were used for ab initio simulations of the TRPES, permitting direct comparison with experiment. For each molecule, the decay of the TRPES signal is characterized by short (30 fs, 52 fs, 23 fs) and long (1.8 ps, 3.5 ps, [306 fs, 18 ps]) time constants for 1,2-butadiene, 1,1-dimethylallene, and tetramethylallene, respectively. However, AIMS simulations show that these time constants are only loosely related to the evolution of electronic character and actually more closely correlate to large amplitude motions on the electronic excited state, modulating the instantaneous vertical ionization potentials. Furthermore, the fully substituted tetramethylallene is observed to undergo qualitatively different dynamics, as displacements involving the relatively massive methyl groups impede direct access to the conical intersections which give rise to the ultrafast relaxation dynamics observed in the other species. These results show that the branching between the “twisting” and “bending” pathways can be modified via the selective methylation of the terminal

  15. Regiodivergent and Stereoselective Hydrosilylation of 1,3-Disubstituted Allenes.

    PubMed

    Miller, Zachary D; Dorel, Ruth; Montgomery, John

    2015-07-27

    Methods for the highly stereoselective and regiodivergent hydrosilylation of 1,3-disubstituted allenes have been developed. The synthesis of E allylsilanes is accomplished with palladium NHC catalysts, and trisubstituted Z alkenylsilanes are accessed with nickel NHC catalysts. Unsymmetrically substituted allenes are well tolerated with nickel catalysis and afford Z alkenylsilanes. Evidence for a plausible mechanism was obtained through an isotopic double-labeling crossover study.

  16. Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights

    SciTech Connect

    Acquaah-Mensah, George K.; Taylor, Ronald C.

    2016-07-01

    Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen BrainAtlasmouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networkswere learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations inmousewhole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, andSyn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD.

  17. Identification of a set of genes showing regionally enriched expression in the mouse brain

    PubMed Central

    D'Souza, Cletus A; Chopra, Vikramjit; Varhol, Richard; Xie, Yuan-Yun; Bohacec, Slavita; Zhao, Yongjun; Lee, Lisa LC; Bilenky, Mikhail; Portales-Casamar, Elodie; He, An; Wasserman, Wyeth W; Goldowitz, Daniel; Marra, Marco A; Holt, Robert A; Simpson, Elizabeth M; Jones, Steven JM

    2008-01-01

    Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression. PMID:18625066

  18. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation

    PubMed Central

    Viader, Andreu; Ogasawara, Daisuke; Joslyn, Christopher M; Sanchez-Alavez, Manuel; Mori, Simone; Nguyen, William; Conti, Bruno; Cravatt, Benjamin F

    2016-01-01

    Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI: http://dx.doi.org/10.7554/eLife.12345.001 PMID:26779719

  19. Reactivity and Chemoselectivity of Allenes in Rh(I)-Catalyzed Intermolecular (5 + 2) Cycloadditions with Vinylcyclopropanes: Allene-Mediated Rhodacycle Formation Can Poison Rh(I)-Catalyzed Cycloadditions

    PubMed Central

    2015-01-01

    Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d−π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes. PMID:25379606

  20. Obituary: James Alfred Van Allen, 1914-2006

    NASA Astrophysics Data System (ADS)

    Ludwig, George H.; McIlwain, Carl Edwin

    2006-12-01

    James Alfred Van Allen, world-renowned space scientist, died 9 August 2006 at the age of ninety-one. He succumbed to heart failure after a ten-week period of declining health. Van Allen served for his entire sixty-seven-year professional career as an amazingly productive researcher, space science spokesman, inspired teacher, and valued colleague. The realization by him and his associates that charged particles are trapped by the Earth's magnetic field began a whole new field of research, magnetospheric physics. Following that initial discovery, he and his associates quickly extended their observations, first to the inner planets, and then to the rest of the planets and beyond. During his tenure at Iowa, he and his group flew instruments on more than sixty successful Earth satellites and planetary spacecraft, including the first missions to the planets Venus, Mars, Jupiter, Saturn, Uranus, and Neptune. Van Allen's lifetime publication list numbers more than 275, of which many are widely-cited, seminal papers. He was the sole author of more than 125 of those papers. Beyond the research laboratory, Van Allen worked energetically throughout his career in establishing space research as a new branch of human inquiry. He was among the most sought-after as a committee member and adviser, working at the highest levels of government, including the White House and Congress, and at all levels of the national and international research establishments. Many presentations in the non-scientific arena helped to bring the exciting discoveries and challenges of space research to the attention of the general public. James Van Allen (Van to his many friends and colleagues) was born on 7 September 1914 on a small farm near Mount Pleasant, Iowa, the second of four sons of Alfred Morris Van Allen and Alma Olney Van Allen. After high school in Mount Pleasant, he entered Iowa Wesleyan College, majoring in physics and graduating summa cum laude. While there, he was introduced to geophysics

  1. On the metallic nature of carbon in allenes and heterocumulenes.

    PubMed

    Alcarazo, Manuel

    2011-03-07

    The IUPAC defines allenes as organic compounds having at least two double bonds from one carbon to two others. Thus the central carbon atom is in accord with the octet rule through the formation of two σ and two π bonds. However, this perspective highlights a series of recent experimental, as well as theoretical results, suggesting that depending on the substituents, this canonical description might not be the most adequate. In fact, in a growing number of examples the bond in allenes and related heterocumulenes is better described as an inner carbon that plays the role of the central atom of a "coordination complex" and interacts with its substituents as if they were ligands of this organic complex. This interpretation of the bond in allenes is especially useful in predicting the C(0), carbene or partial carbocationic character of the central carbon atom.

  2. Clarence Allen talks about the responsibilities in earthquake prediction

    USGS Publications Warehouse

    Spall, H.

    1978-01-01

    Dr. Clarence R. Allen is professor of geology and geophysics at the California Institute of Technology. He has been a member of advisory panels to the Executive Office of the President, National Academy of Sciences, National Science Foundation, U.S Geological Survey, UNESCO, California State Mining and Geology Board, and the California Department of Water Resources. Dr. Allen has been President of both the Geological Society of America and the Seismological Society of America (SSA). The title of this interview is based on his presidential address to the SSA in 1976. 

  3. Neonatal atlas construction using sparse representation.

    PubMed

    Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H; Lin, Weili; Shen, Dinggang

    2014-09-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases.

  4. The optimal pallidal target in deep brain stimulation for dystonia: a study using a functional atlas based on non-linear image registration

    PubMed Central

    Tolleson, Christopher; Pallavaram, Srivatsan; Li, Chen; Fang, John; Phibbs, Fenna; Konrad, Peter; Hedera, Peter; Francois-D'Haese, Pierre; Dawant, Benoit M.; Davis, Thomas L.

    2014-01-01

    Background Deep Brain Stimulation (DBS) of the globus pallidus interna (GPi) is established as efficacious for dystonia yet the optimal target within this structure is not well defined. Published evidence suggests that spatial normalization provides a better estimate of DBS lead location than traditional methods based on standard stereotactic coordinates. Methods We retrospectively reviewed our pallidal implanted dystonia population. Patient imaging scans were morphed into an MRI atlas using a non-linear image registration algorithm. Active contact locations were projected onto the atlas and clusters analyzed for the degree of variance in two groups: 1) good and poor responders and 2) cervical (CD) and generalized dystonia (GD). Results Average active contact location between CD and GD good responders was distinct but not significantly different. Mean active contact for CD poor responders was significantly different from CD responders and GD poor responders in the dorsoventral direction. Conclusions A normalized imaging space is arguably more accurate in visualizing postoperative leads. Despite some separation between groups, this data suggests there was not an optimal pallidal target for common dystonia patients. Degrees of variance overlapped due to a large degree of individual target variation. Patient selection may ultimately be the key to maximizing patient outcomes. PMID:25502118

  5. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

    PubMed

    Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

    2013-11-15

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray

  6. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain.

    PubMed

    Chou, Shen-Ju; Wang, Chindi; Sintupisut, Nardnisa; Niou, Zhen-Xian; Lin, Chih-Hsu; Li, Ker-Chau; Yeang, Chen-Hsiang

    2016-01-20

    Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development.

  7. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry

    PubMed Central

    Tadayon, Sayed H.; Vaziri-Pashkam, Maryam; Kahali, Pegah; Ansari Dezfouli, Mitra; Abbassian, Abdolhossein

    2016-01-01

    Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (PCombined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry. PMID:27252636

  8. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry.

    PubMed

    Tadayon, Sayed H; Vaziri-Pashkam, Maryam; Kahali, Pegah; Ansari Dezfouli, Mitra; Abbassian, Abdolhossein

    2016-01-01

    Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (P Combined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry.

  9. 5. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Historic American Buildings Survey Harold Allen, Photographer June 1964 TRIPLE STAINED GLASS WINDOWS AND COLUMN SUPPORTING BALCONY (EAST WINDOWS IN SOUTH WALL OF MAIN FLOOR OF AUDITORIUM) - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  10. Van Allen Probes Science Gateway: A Centralized Data Access Point

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Ukhorskiy, A. Y.; Sotirelis, T.; Stephens, G. K.; Kessel, R.; Potter, M.

    2015-12-01

    The Van Allen Probes Science Gateway acts a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the Van Allen Probes Space Weather data to users. Over the past years, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes science and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including, simple time series, data plotted as a function of orbital location, and time versus L-Shell, capability of visualizing data from both probes (A & B) on the same plot. In cooperation with all Van Allen Probes Instrument SOCs, the Science Gateway will soon be able to serve higher level data products (Level 3), and to visualize them via the above mentioned HTML5 interface. Users will also be able to create customized CDF files on the fly.

  11. The Evolving Space Weather System—Van Allen Probes Contribution

    NASA Astrophysics Data System (ADS)

    Zanetti, L. J.; Mauk, B. H.; Fox, N. J.; Barnes, R. J.; Weiss, M.; Sotirelis, T. S.; Raouafi, N.-E.; Kessel, R. L.; Becker, H. N.

    2014-10-01

    The overarching goal and purpose of the study of space weather is clear—to understand and address the issues caused by solar disturbances on humans and technological systems. Space weather has evolved in the past few decades from a collection of concerned agencies and researchers to a critical function of the National Weather Service of NOAA. The general effects have also evolved from the well-known telegraph disruptions of the mid-1800s to modern day disturbances of the electric power grid, communications and navigation, human spaceflight and spacecraft systems. The last two items in this list, and specifically the effects of penetrating radiation, were the impetus for the space weather broadcast implemented on NASA's Van Allen Probes' twin pair of satellites, launched in August of 2012 and orbiting directly through Earth's severe radiation belts. The Van Allen Probes mission, formerly the Radiation Belt Storm Probes (RBSP), was renamed soon after launch to honor the discoverer of Earth's radiation belts at the beginning of the space age, the late James Van Allen (the spacecraft themselves are still referred to as RBSP-A and RBSP-B). The Van Allen Probes are one part of NASA's Living With a Star program formulated to advance the scientific understanding of the connection between solar disturbances, the resulting heliospheric conditions, and their effects on the geospace and Earth environment.

  12. Sensitivity analysis and automation for intraoperative implementation of the atlas-based method for brain shift correction

    NASA Astrophysics Data System (ADS)

    Chen, Ishita; Simpson, Amber L.; Sun, Kay; Thompson, Reid C.; Miga, Michael I.

    2013-03-01

    The use of biomechanical models to correct the misregistration due to deformation in image guided neurosurgical systems has been a growing area of investigation. In previous work, an atlas-based inverse model was developed to account for soft-tissue deformations during image-guided surgery. Central to that methodology is a considerable amount of pre-computation and planning. The goal of this work is to evaluate techniques that could potentially reduce that burden. Distinct from previous manual techniques, an automated segmentation technique is described for the cerebrum and dural septa. The shift correction results using this automated segmentation method were compared to those using the manual methods. In addition, the extent and distribution of the surgical parameters associated with the deformation atlas were investigated by a sensitivity analysis using simulation experiments and clinical data. The shift correction results did not change significantly using the automated method (correction of 73+/-13% ) as compared to the semi-automated method from previous work (correction of 76+/-13%). The results of the sensitivity analysis show that the atlas could be constructed by coarser sampling (six fold reduction) without substantial degradation in the shift reconstruction, a decrease in preoperative computational time from 13.1+/-3.5 hours to 2.2+/-0.6 hours. The automated segmentation technique and the findings of the sensitivity study have significant impact on the reduction of pre-operative computational time, improving the utility of the atlas-based method. The work in this paper suggests that the atlas-based technique can become a `time of surgery' setup procedure rather than a pre-operative computing strategy.

  13. The EF-hand Ca(2+)-binding protein super-family: a genome-wide analysis of gene expression patterns in the adult mouse brain.

    PubMed

    Girard, F; Venail, J; Schwaller, B; Celio, M R

    2015-05-21

    In mice, 249 putative members of the superfamily of EF-hand domain Ca(2+)-binding proteins, manifesting great diversity in structure, cellular localization and functions have been identified. Three members in particular, namely, calbindin-D28K, calretinin and parvalbumin, are widely used as markers for specific neuronal subpopulations in different regions of the brain. The aim of the present study was to compile a comprehensive atlas of the gene-expression profiles of the entire EF-hand gene superfamily in the murine brain. This was achieved by a meticulous examination of the in-situ hybridization images in the Allen Brain Atlas database. Topographically, our analysis focused on the olfactory bulb, cerebral cortex (barrel cortex in the primary somatosensory area), basal ganglia, hippocampus, amygdala, thalamus, hypothalamus, cerebellum, midbrain, pons and medulla, and on clearly identifiable sub-structures within each of these areas. The expression profiles of four family-members, namely hippocalcin-like 4, neurocalcin-δ, plastin 3 and tescalcin, that have not been hitherto reported, at either the mRNA (in-situ-hybridization) or the protein (immunohistochemical) levels, are now presented for the first time. The fruit of our analysis is a document in which the gene-expression profiles of all members of the EF-hand family genes are compared, and in which future possible neuronal markers for specific cells/brain areas are identified. The assembled information could afford functional clues to investigators, conducive to further experimental pursuit.

  14. Isomer-specific combustion chemistry in allene and propyne flames

    SciTech Connect

    Hansen, Nils; Miller, James A.; Westmoreland, Phillip R.; Kasper, Tina; Kohse-Hoeinghaus, Katharina; Wang, Juan; Cool, Terrill A.

    2009-11-15

    A combined experimental and modeling study is performed to clarify the isomer-specific combustion chemistry in flames fueled by the C{sub 3}H{sub 4} isomers allene and propyne. To this end, mole fraction profiles of several flame species in stoichiometric allene (propyne)/O{sub 2}/Ar flames are analyzed by means of a chemical kinetic model. The premixed flames are stabilized on a flat-flame burner under a reduced pressure of 25 Torr (=33.3 mbar). Quantitative species profiles are determined by flame-sampling molecular-beam mass spectrometry, and the isomer-specific flame compositions are unraveled by employing photoionization with tunable vacuum-ultraviolet synchrotron radiation. The temperature profiles are measured by OH laser-induced fluorescence. Experimental and modeled mole fraction profiles of selected flame species are discussed with respect to the isomer-specific combustion chemistry in both flames. The emphasis is put on main reaction pathways of fuel consumption, of allene and propyne isomerization, and of isomer-specific formation of C{sub 6} aromatic species. The present model includes the latest theoretical rate coefficients for reactions on a C{sub 3}H{sub 5} potential [J.A. Miller, J.P. Senosiain, S.J. Klippenstein, Y. Georgievskii, J. Phys. Chem. A 112 (2008) 9429-9438] and for the propargyl recombination reactions [Y. Georgievskii, S.J. Klippenstein, J.A. Miller, Phys. Chem. Chem. Phys. 9 (2007) 4259-4268]. Larger peak mole fractions of propargyl, allyl, and benzene are observed in the allene flame than in the propyne flame. In these flames virtually all of the benzene is formed by the propargyl recombination reaction. (author)

  15. Van Allen Probes Science Gateway and Space Weather Data Processing

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2014-12-01

    The Van Allen Probes Science Gateway acts as a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the VAP Space Weather data to users. Over the past year, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes summary and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including simple time series, data plotted as a function of orbital location, and time versus L-Shell. We discuss the new Van Allen Probes Science Gateway and the Space Weather Data Pipeline.

  16. A method based on Monte Carlo simulations and voxelized anatomical atlases to evaluate and correct uncertainties on radiotracer accumulation quantitation in beta microprobe studies in the rat brain

    NASA Astrophysics Data System (ADS)

    Pain, F.; Dhenain, M.; Gurden, H.; Routier, A. L.; Lefebvre, F.; Mastrippolito, R.; Lanièce, P.

    2008-10-01

    The β-microprobe is a simple and versatile technique complementary to small animal positron emission tomography (PET). It relies on local measurements of the concentration of positron-labeled molecules. So far, it has been successfully used in anesthetized rats for pharmacokinetics experiments and for the study of brain energetic metabolism. However, the ability of the technique to provide accurate quantitative measurements using 18F, 11C and 15O tracers is likely to suffer from the contribution of 511 keV gamma rays background to the signal and from the contribution of positrons from brain loci surrounding the locus of interest. The aim of the present paper is to provide a method of evaluating several parameters, which are supposed to affect the quantification of recordings performed in vivo with this methodology. We have developed realistic voxelized phantoms of the rat whole body and brain, and used them as input geometries for Monte Carlo simulations of previous β-microprobe reports. In the context of realistic experiments (binding of 11C-Raclopride to D2 dopaminergic receptors in the striatum; local glucose metabolic rate measurement with 18F-FDG and H2O15 blood flow measurements in the somatosensory cortex), we have calculated the detection efficiencies and corresponding contribution of 511 keV gammas from peripheral organs accumulation. We confirmed that the 511 keV gammas background does not impair quantification. To evaluate the contribution of positrons from adjacent structures, we have developed β-Assistant, a program based on a rat brain voxelized atlas and matrices of local detection efficiencies calculated by Monte Carlo simulations for several probe geometries. This program was used to calculate the 'apparent sensitivity' of the probe for each brain structure included in the detection volume. For a given localization of a probe within the brain, this allows us to quantify the different sources of beta signal. Finally, since stereotaxic accuracy is

  17. Anatomy atlases.

    PubMed

    Rosse, C

    1999-01-01

    Anatomy atlases are unlike other knowledge sources in the health sciences in that they communicate knowledge through annotated images without the support of narrative text. An analysis of the knowledge component represented by images and the history of anatomy atlases suggest some distinctions that should be made between atlas and textbook illustrations. Textbook and atlas should synergistically promote the generation of a mental model of anatomy. The objective of such a model is to support anatomical reasoning and thereby replace memorization of anatomical facts. Criteria are suggested for selecting anatomy texts and atlases that complement one another, and the advantages and disadvantages of hard copy and computer-based anatomy atlases are considered.

  18. Differences in resting state regional cerebral blood flow assessed with 99mTc-HMPAO SPECT and brain atlas matching between depressed patients with and without tinnitus.

    PubMed

    Gardner, A; Pagani, M; Jacobsson, H; Lindberg, G; Larsson, S A; Wägner, A; Hällstrom, T

    2002-05-01

    An increased occurrence of major depressive disorder has been reported in tinnitus patients, and of tinnitus in depressive patients. Involvement of several Brodmann areas (BAs) has been reported in tinnitus perception. The aim of this study was to assess the regional cerebral blood flow (rCBF) changes in depressed patients with and without tinnitus. The rCBF distribution at rest was compared among 45 patients with a lifetime prevalence of major depressive disorder, of whom 27 had severe tinnitus, and 26 normal healthy subjects. 99mTc-hexamethylenepropylene amine oxime (99mTc-HMPAO) single photon emission computed tomography (SPECT), using a three-headed gamma camera, was performed and the uptake in 34 functional sub-volumes of the brain bilaterally was assessed by a computerized brain atlas. Decreased rCBF in right frontal lobe BA 45 (P<0.05), the left parietal lobe BA 39 (P<0.00) and the left visual association cortex BA 18 (P<0.05) was found in tinnitus patients compared with non-tinnitus patients. The proportion of tinnitus patients with pronounced rCBF alterations in one or more of the temporal lobe BAs 41+21+22 was increased compared to gender matched controls (P<0.00) and patients without tinnitus (P<0.05). Positive correlations were found between trait anxiety scales from the Karolinska Scales of Personality and rCBF in tinnitus patients only in three limbic BAs (P<0.01), and inverse correlations in non-tinnitus patients only in five BAs subserving auditory perception and processing (P<0.05). rCBF differences between healthy controls and depressed patients with and without tinnitus were found in this study. The rCBF alterations were distributed in the cortex and were particularly specific in the auditory cortex. These findings suggest that taking audiological symptoms into account may yield more consistent results between rCBF studies of depression.

  19. Galactic Plane SETI Observations with the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Backus, P. R.; Tarter, J. C.; Davis, M. M.; Jordan, J. C.; Kilsdonk, T. N.; Shostak, G. S.; Ackerman, R.; DeBoer, D. R.; Dreher, J. W.; Harp, G. R.; Ross, J. E.; Stauduhar, R.

    2005-12-01

    In the spring of 2006, the Allen Telescope Array (ATA), a joint effort of the U.C. Berkeley Radio Astronomy Lab and the SETI Institute, will begin initial operations. Starting with 42 antennas out of a planned 350, the array will be equivalent to a single 40 meter dish. Using three phased beams, we will survey twenty square degrees around the galactic center for narrowband signals in the frequency range from 1410 to 1730 MHz (the "Water Hole"). Comparison of results from the beams will be used to eliminate signals from terrestrial and satellite sources. At these frequencies, the wide field of view of the array allows us to cover the 2 x 10 degree strip with five antenna positions. The field of view will track one of the five positions for up to five hours, while the phased beams are pointed within the field of view for 98 seconds per 20 MHz frequency band. During these SETI observations spanning approximately seven months, other radio astronomy observations of this very interesting region will run in parallel using two other independently tunable IF systems with a correlator and other phase array beams feeding other backend processors. Construction of the ATA is supported by private funding, primarily from the Paul G. Allen Foundation. The correlator for the ATA is supported by NSF Grant AST-0322309 to the UCB Radio Astronomy Lab.

  20. A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

    PubMed Central

    Nitzsche, Björn; Frey, Stephen; Collins, Louis D.; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H.; Fonov, Vladimir S.; Boltze, Johannes

    2015-01-01

    Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

  1. A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes.

    PubMed

    Nitzsche, Björn; Frey, Stephen; Collins, Louis D; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H; Fonov, Vladimir S; Boltze, Johannes

    2015-01-01

    Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species.

  2. mRNA Transcriptomics of Galectins Unveils Heterogeneous Organization in Mouse and Human Brain.

    PubMed

    John, Sebastian; Mishra, Rashmi

    2016-01-01

    Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies. Results: In order to fill this crucial gap in our understanding of brain galectins, we analyzed the in situ hybridization and microarray data of adult mouse and human brain respectively, from the Allen Brain Atlas, to resolve each galectin-subtype's spatial distribution across brain distinct cytoarchitecture. Next, transcription factors (TFs) that may regulate galectins were identified using TRANSFAC software and the list obtained was further curated to sort TFs on their confirmed transcript expression in the adult brain. Galectin-TF cluster analysis, gene-ontology annotations and co-expression networks were then extrapolated to predict distinct functional relevance of each galectin in the neuronal processes. Data shows that galectins have highly heterogeneous expression within and across brain sub-structures and are predicted to be the crucial targets of brain enriched TFs. Lgals9 had maximal spatial distribution across mouse brain with inferred predominant roles in neurogenesis while LGALS1 was ubiquitously expressed in human. Limbic region associated with learning, memory and emotions and substantia nigra associated with motor movements showed strikingly high expression of LGALS1 and LGALS8 in human vs. mouse brain. The overall expression profile of galectin-8 was most preserved across both these

  3. mRNA Transcriptomics of Galectins Unveils Heterogeneous Organization in Mouse and Human Brain

    PubMed Central

    John, Sebastian; Mishra, Rashmi

    2016-01-01

    Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies. Results: In order to fill this crucial gap in our understanding of brain galectins, we analyzed the in situ hybridization and microarray data of adult mouse and human brain respectively, from the Allen Brain Atlas, to resolve each galectin-subtype’s spatial distribution across brain distinct cytoarchitecture. Next, transcription factors (TFs) that may regulate galectins were identified using TRANSFAC software and the list obtained was further curated to sort TFs on their confirmed transcript expression in the adult brain. Galectin-TF cluster analysis, gene-ontology annotations and co-expression networks were then extrapolated to predict distinct functional relevance of each galectin in the neuronal processes. Data shows that galectins have highly heterogeneous expression within and across brain sub-structures and are predicted to be the crucial targets of brain enriched TFs. Lgals9 had maximal spatial distribution across mouse brain with inferred predominant roles in neurogenesis while LGALS1 was ubiquitously expressed in human. Limbic region associated with learning, memory and emotions and substantia nigra associated with motor movements showed strikingly high expression of LGALS1 and LGALS8 in human vs. mouse brain. The overall expression profile of galectin-8 was most preserved across both these

  4. Evaluation of Atlas-Based White Matter Segmentation with Eve

    PubMed Central

    Plassard, Andrew J.; Hinton, Kendra E.; Venkatraman, Vijay; Gonzalez, Christopher; Resnick, Susan M.; Landman, Bennett A.

    2015-01-01

    Multi-atlas labeling has come in wide spread use for whole brain labeling on magnetic resonance imaging. Recent challenges have shown that leading techniques are near (or at) human expert reproducibility for cortical gray matter labels. However, these approaches tend to treat white matter as essentially homogeneous (as white matter exhibits isointense signal on structural MRI). The state-of-the-art for white matter atlas is the single-subject Johns Hopkins Eve atlas. Numerous approaches have attempted to use tractography and/or orientation information to identify homologous white matter structures across subjects. Despite success with large tracts, these approaches have been plagued by difficulties in with subtle differences in course, low signal to noise, and complex structural relationships for smaller tracts. Here, we investigate use of atlas-based labeling to propagate the Eve atlas to unlabeled datasets. We evaluate single atlas labeling and multi-atlas labeling using synthetic atlases derived from the single manually labeled atlas. On 5 representative tracts for 10 subjects, we demonstrate that (1) single atlas labeling generally provides segmentations within 2mm mean surface distance, (2) morphologically constraining DTI labels within structural MRI white matter reduces variability, and (3) multi-atlas labeling did not improve accuracy. These efforts present a preliminary indication that single atlas labels with correction is reasonable, but caution should be applied. To purse multi-atlas labeling and more fully characterize overall performance, more labeled datasets would be necessary. PMID:25914503

  5. Evaluation of Atlas-Based White Matter Segmentation with Eve.

    PubMed

    Plassard, Andrew J; Hinton, Kendra E; Venkatraman, Vijay; Gonzalez, Christopher; Resnick, Susan M; Landman, Bennett A

    2015-03-20

    Multi-atlas labeling has come in wide spread use for whole brain labeling on magnetic resonance imaging. Recent challenges have shown that leading techniques are near (or at) human expert reproducibility for cortical gray matter labels. However, these approaches tend to treat white matter as essentially homogeneous (as white matter exhibits isointense signal on structural MRI). The state-of-the-art for white matter atlas is the single-subject Johns Hopkins Eve atlas. Numerous approaches have attempted to use tractography and/or orientation information to identify homologous white matter structures across subjects. Despite success with large tracts, these approaches have been plagued by difficulties in with subtle differences in course, low signal to noise, and complex structural relationships for smaller tracts. Here, we investigate use of atlas-based labeling to propagate the Eve atlas to unlabeled datasets. We evaluate single atlas labeling and multi-atlas labeling using synthetic atlases derived from the single manually labeled atlas. On 5 representative tracts for 10 subjects, we demonstrate that (1) single atlas labeling generally provides segmentations within 2mm mean surface distance, (2) morphologically constraining DTI labels within structural MRI white matter reduces variability, and (3) multi-atlas labeling did not improve accuracy. These efforts present a preliminary indication that single atlas labels with correction is reasonable, but caution should be applied. To purse multi-atlas labeling and more fully characterize overall performance, more labeled datasets would be necessary.

  6. Astronauts Gardner and Allen during loading of Westar VI in payload bay

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen IV, top, hangs onto a stinger device as Astronaut Dale A. Gardner in the cargo bay of Discovery waits to assist in the berthing of the previously stranded satellite. The end effector of the remote manipulator system (RMS), controlled from inside the Discovery'S cabin, grasps a special grapple point to Allen's right.

  7. Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-75 ONBOARD VIEW --- Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the flight deck of the Space Shuttle Columbia. Allen was joined by four other astronauts and an international payload specialist for more than 16 days of research aboard Columbia. The photograph was taken with a 70mm handheld camera.

  8. Q & A with Ed Tech Leaders: Interview with Michael W. Allen

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.

    2014-01-01

    Michael W. Allen, the Chairman and CEO of Allen Interactions, is an architect of interactive multimedia learning and is recognized for his many insights, inventions, and presentations. With over 50 years of experience in e-learning, both in academic and corporate settings, he is known for his role in creating Authorware and overseeing the work of…

  9. Allen Ivey: Pioneer in Counseling Theory and Practice, and Crusader for Multiculturalism and Social Justice

    ERIC Educational Resources Information Center

    Santiago-Rivera, Azara L.

    2009-01-01

    This article reviews the groundbreaking work of Dr. Allen Ivey through a personal interview and conversations with Mary Bradford Ivey, including a number of colleagues and former students. Allen's enormous contribution to the counseling profession spans nearly four decades. Although best known for microcounseling skills, which is widely taught in…

  10. Meeting the Challenge of Intermolecular Gold(I)-Catalyzed Cycloadditions of Alkynes and Allenes

    PubMed Central

    Muratore, Michael E; Homs, Anna; Obradors, Carla; Echavarren, Antonio M

    2014-01-01

    The development of gold(I)-catalyzed intermolecular carbo- and hetero-cycloadditions of alkynes and allenes has been more challenging than their intramolecular counterparts. Here we review, with a mechanistic perspective, the most fundamental intermolecular cycloadditions of alkynes and allenes with alkenes. PMID:25048645

  11. Optimization of large-scale mouse brain connectome via joint evaluation of DTI and neuron tracing data.

    PubMed

    Chen, Hanbo; Liu, Tao; Zhao, Yu; Zhang, Tuo; Li, Yujie; Li, Meng; Zhang, Hongmiao; Kuang, Hui; Guo, Lei; Tsien, Joe Z; Liu, Tianming

    2015-07-15

    Tractography based on diffusion tensor imaging (DTI) data has been used as a tool by a large number of recent studies to investigate structural connectome. Despite its great success in offering unique 3D neuroanatomy information, DTI is an indirect observation with limited resolution and accuracy and its reliability is still unclear. Thus, it is essential to answer this fundamental question: how reliable is DTI tractography in constructing large-scale connectome? To answer this question, we employed neuron tracing data of 1772 experiments on the mouse brain released by the Allen Mouse Brain Connectivity Atlas (AMCA) as the ground-truth to assess the performance of DTI tractography in inferring white matter fiber pathways and inter-regional connections. For the first time in the neuroimaging field, the performance of whole brain DTI tractography in constructing a large-scale connectome has been evaluated by comparison with tracing data. Our results suggested that only with the optimized tractography parameters and the appropriate scale of brain parcellation scheme, can DTI produce relatively reliable fiber pathways and a large-scale connectome. Meanwhile, a considerable amount of errors were also identified in optimized DTI tractography results, which we believe could be potentially alleviated by efforts in developing better DTI tractography approaches. In this scenario, our framework could serve as a reliable and quantitative test bed to identify errors in tractography results which will facilitate the development of such novel tractography algorithms and the selection of optimal parameters.

  12. Chirality Transfer in Gold(I)‐Catalysed Hydroalkoxylation of 1,3‐Disubstituted Allenes

    PubMed Central

    Webster, Stacey; Sutherland, Daniel R.

    2016-01-01

    Abstract Gold(I)‐catalysed intermolecular hydroalkoxylation of enantioenriched 1,3‐disubstituted allenes was previously reported to occur with poor chirality transfer due to rapid allene racemisation. The first intermolecular hydroalkoxylation of allenes with efficient chirality transfer is reported here, exploiting conditions that suppress allene racemisation. A full substrate scope study reveals that excellent regio‐ and stereoselectivities are achieved when a σ‐withdrawing substituent is present. PMID:27862422

  13. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  14. New Cooled Feeds for the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Welch, Wm. J.; Fleming, Matthew; Munson, Chris; Tarter, Jill; Harp, G. R.; Spencer, Robert; Wadefalk, Niklas

    2017-04-01

    We developed a new generation of low-noise, broadband feeds for the Allen Telescope Array at the Hat Creek Observatory in Northern California. The new feeds operate over the frequency range 0.9 to 14 GHz. The noise temperatures of the feeds have been substantially improved by cooling the entire feed structure as well as the low-noise amplifiers to 70 K. To achieve this improved performance, the new feeds are mounted in glass vacuum bottles with plastic lenses that maximize the microwave transmission through the bottles. Both the cooled feeds and their low-noise amplifiers produce total system temperatures that are in the range 25–30 K from 1 GHz to 5 GHz and 40–50 K up to 12.5 GHz.

  15. Van Allen Probe Charging During the St. Patrick's Day Event

    NASA Technical Reports Server (NTRS)

    Parker, L. Neergaard; Minow, J. I.

    2015-01-01

    The geomagnetic storms on and around March 17, 2015 marked the largest storms seen in the declining phase of the solar cycle to date. We use the Helium Oxygen Proton Electron (HOPE) mass spectrometer on board the Van Allen Probe - A and B satellites to study in detail the charging effects seen on these spacecraft during this time. Ion particle flux data provides information on the magnitude of the charging events using the ion line charging signature due to low energy ions accelerated by the spacecraft potential. Electron flux observations are used to correlate the charging environment with variations in spacecraft potential through the event. We also investigate the density and temperature of ions and electrons during the time of the charging event.

  16. Van Allen Probe Charging During the St. Patrick's Day Event

    NASA Astrophysics Data System (ADS)

    Parker, L. N.; Minow, J. I.

    2015-12-01

    The geomagnetic storms on and around March 17, 2015 marked the largest storms seen in the declining phase of the solar cycle to date. We use the Helium Oxygen Proton Electron (HOPE) mass spectrometer on board the Van Allen Probe - A and B satellites to study in detail the charging effects seen on these spacecraft during this time. Ion particle flux data provides information on the magnitude of the charging events using the ion line charging signature due to low energy ions accelerated by the spacecraft potential. Electron flux observations are used to correlate the charging environment with variations in spacecraft potential through the event. We also investigate the density and temperature of ions and electrons during the time of the charging event.

  17. Computerized atlas for functional stereotaxis

    NASA Astrophysics Data System (ADS)

    Hardy, Tyrone L.; Brynildson, L. R. D.

    1993-09-01

    Our original brain mapping techniques have been expanded so that MR and CT images can be displayed in a three-dimensionally simulated localization environment. Various combinations of MR images as well as CT images (or combinations of both and angiography) can be selectively displayed and viewed in three-dimensional stereotactic space. Data from the Talairach anatomical library, the architectonics of the atlases of Van Buren and Borke, Schaltenbrand and Bailey, Schaltenbrand and Wahren, and Brodmann's cortico-architectonics have been used to develop a detailed anatomical atlas library and brain mapping system based on brain reference structures common to each of these databases. The data in this mapping and imaging environment can be interrogated to create computerized anatomical displays showing any given functional anatomical region in two-dimensional displays or three-dimensional relief. This composite mapping system allows the interrogation and cross referencing of data from virtually any other brain mapping or localization system.

  18. Brain microstructural development at near-term age in very-low-birth-weight preterm infants: an atlas-based diffusion imaging study.

    PubMed

    Rose, Jessica; Vassar, Rachel; Cahill-Rowley, Katelyn; Guzman, Ximena Stecher; Stevenson, David K; Barnea-Goraly, Naama

    2014-02-01

    At near-term age the brain undergoes rapid growth and development. Abnormalities identified during this period have been recognized as potential predictors of neurodevelopment in children born preterm. This study used diffusion tensor imaging (DTI) to examine white matter (WM) microstructure in very-low-birth-weight (VLBW) preterm infants to better understand regional WM developmental trajectories at near-term age. DTI scans were analyzed in a cross-sectional sample of 45 VLBW preterm infants (BW≤1500g, GA≤32weeks) within a cohort of 102 neonates admitted to the NICU and recruited to participate prior to standard-of-care MRI, from 2010 to 2011, 66/102 also had DTI. For inclusion in this analysis, 45 infants had DTI, no evidence of brain abnormality on MRI, and were scanned at PMA ≤40weeks (34.7-38.6). White matter microstructure was analyzed in 19 subcortical regions defined by DiffeoMap neonatal brain atlas, using threshold values of trace <0.006mm(2)s(-1) and FA >0.15. Regional fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were calculated and temporal-spatial trajectories of development were examined in relation to PMA and brain region location. Posterior regions within the corona radiata (CR), corpus callosum (CC), and internal capsule (IC) demonstrated significantly higher mean FA values compared to anterior regions. Posterior regions of the CR and IC demonstrated significantly lower RD values compared to anterior regions. Centrally located projection fibers demonstrated higher mean FA and lower RD values than peripheral regions including the posterior limb of the internal capsule (PLIC), cerebral peduncle, retrolenticular part of the IC, posterior thalamic radiation, and sagittal stratum. Centrally located association fibers of the external capsule had higher FA and lower RD than the more peripherally-located superior longitudinal fasciculus (SLF). A significant relationship between PMA-at-scan and

  19. Neonatal brain image segmentation in longitudinal MRI studies.

    PubMed

    Shi, Feng; Fan, Yong; Tang, Songyuan; Gilmore, John H; Lin, Weili; Shen, Dinggang

    2010-01-01

    In the study of early brain development, tissue segmentation of neonatal brain MR images remains challenging because of the insufficient image quality due to the properties of developing tissues. Among various brain tissue segmentation algorithms, atlas-based brain image segmentation can potentially achieve good segmentation results on neonatal brain images. However, their performances rely on both the quality of the atlas and the spatial correspondence between the atlas and the to-be-segmented image. Moreover, it is difficult to build a population atlas for neonates due to the requirement of a large set of tissue-segmented neonatal brain images. To combat these obstacles, we present a longitudinal neonatal brain image segmentation framework by taking advantage of the longitudinal data acquired at late time-point to build a subject-specific tissue probabilistic atlas. Specifically, tissue segmentation of the neonatal brain is formulated as two iterative steps of bias correction and probabilistic-atlas-based tissue segmentation, along with the longitudinal atlas reconstructed by the late time image of the same subject. The proposed method has been evaluated qualitatively through visual inspection and quantitatively by comparing with manual delineations and two population-atlas-based segmentation methods. Experimental results show that the utilization of a subject-specific probabilistic atlas can substantially improve tissue segmentation of neonatal brain images.

  20. Quantitative atlas of blood-brain barrier transporters, receptors, and tight junction proteins in rats and common marmoset.

    PubMed

    Hoshi, Yutaro; Uchida, Yasuo; Tachikawa, Masanori; Inoue, Takashi; Ohtsuki, Sumio; Terasaki, Tetsuya

    2013-09-01

    The purpose of this study was to determine the protein amounts of blood-brain barrier (BBB) permeability-related transporters, receptors, and tight junction proteins in Sprague Dawley and Wistar rats and common marmoset, and also to investigate inter-species and inter-strain differences across rodents and primates. Quantification of target proteins in isolated brain capillaries was conducted by liquid chromatography-tandem mass spectrometry-based quantitative targeted absolute proteomics, with in silico peptide selection. Most target proteins showed inter-rodent, inter-primate species, and inter-rat strain differences of less than 2-fold. Comparison of rat and human BBB showed that P-glycoprotein, multidrug resistance-associated protein 4, monocarboxylate transporter 1, l-type amino acid transporter, and organic anion transporter 3 exhibited differences of more than two-fold in protein abundance, whereas the amounts of breast cancer resistance protein, glucose transporter 1, and insulin receptor were similar in rat and human. In contrast, the differences between marmoset and human BBB were less than 2-fold for almost all measured proteins. Thus, the molecular basis of BBB functions may be similar in marmoset and human, whereas that of rats shows significant differences. The marmoset may be a good model to access in vivo human BBB permeability characteristics, as an alternative to rat and macaque monkey.

  1. A simple approach to separate a mixture of homopropargylic and allenic alcohols.

    PubMed

    Fu, Fan; Hoang, Kim Le Mai; Loh, Teck-Peng

    2008-08-21

    A simple and practical approach to separate homopropargylic alcohol from allenic alcohol has been developed. It involves the formation of an insoluble silver acetylide species between silver nitrate and homopropargylic alcohol in aqueous acetone which can be separated from the allenic alcohol through a simple filtration. The homopropargylic alcohol can subsequently be recovered by hydrolysis with 1 N HCl. This protocol has been applied to the separation of a mixture of chiral homopropargylic and allenic alcohols in excellent yields with retention of absolute stereochemistry.

  2. Orion GNC Mitigation Efforts for Van Allen Radiation

    NASA Technical Reports Server (NTRS)

    King, Ellis T.; Jackson, Mark

    2013-01-01

    The Orion Crew Module (CM) is NASA's next generation manned space vehicle, scheduled to return humans to lunar orbit in the coming decade. The Orion avionics and GN&C architectures have progressed through a number of project phases and are nearing completion of a major milestone. The first unmanned test mission, dubbed "Exploration Flight Test One" (EFT-1) is scheduled to launch from NASA Kennedy Space Center late next year and provides the first integrated test of all the vehicle systems, avionics and software. The EFT-1 mission will be an unmanned test flight that includes a high speed re-entry from an elliptical orbit, which will be launched on an expendable launch vehicle (ELV). The ELV will place CM and the ELV upper stage into a low Earth orbit (LEO) for one revolution. After the first LEO, the ELV upper stage will re-ignite and place the combined upper stage/CM into an elliptical orbit whose perigee results in a high energy entry to test CM response in a relatively high velocity, high heating environment. While not producing entry velocities as high as those experienced in returning from a lunar orbit, the trajectory was chosen to provide higher stresses on the thermal protection and guided entry systems, as compared against a lower energy LEO entry. However the required entry geometry with constraints on inclination and landing site result in a trajectory that lingers for many hours in the Van Allen radiation belts. This exposes the vehicle and avionics to much higher levels of high energy proton radiation than a typical LEO or lunar trajectory would encounter. As a result, Van Allen radiation poses a significant risk to the Orion avionics system, and particularly the Flight Control Module (FCM) computers that house the GN&C flight software. The measures taken by the Orion GN&C, Flight Software and Avionics teams to mitigate the risks associated with the Van Allen radiation on EFT-1 are covered in the paper. Background on the Orion avionics subsystem is

  3. Regional expression of the MAPT gene is associated with loss of hubs in brain networks and cognitive impairment in Parkinson disease and progressive supranuclear palsy.

    PubMed

    Rittman, Timothy; Rubinov, Mikail; Vértes, Petra E; Patel, Ameera X; Ginestet, Cedric E; Ghosh, Boyd C P; Barker, Roger A; Spillantini, Maria Grazia; Bullmore, Edward T; Rowe, James B

    2016-12-01

    Abnormalities of tau protein are central to the pathogenesis of progressive supranuclear palsy, whereas haplotype variation of the tau gene MAPT influences the risk of Parkinson disease and Parkinson's disease dementia. We assessed whether regional MAPT expression might be associated with selective vulnerability of global brain networks to neurodegenerative pathology. Using task-free functional magnetic resonance imaging in progressive supranuclear palsy, Parkinson disease, and healthy subjects (n = 128), we examined functional brain networks and measured the connection strength between 471 gray matter regions. We obtained MAPT and SNCA microarray expression data in healthy subjects from the Allen brain atlas. Regional connectivity varied according to the normal expression of MAPT. The regional expression of MAPT correlated with the proportionate loss of regional connectivity in Parkinson's disease. Executive cognition was impaired in proportion to the loss of hub connectivity. These effects were not seen with SNCA, suggesting that alpha-synuclein pathology is not mediated through global network properties. The results establish a link between regional MAPT expression and selective vulnerability of functional brain networks to neurodegeneration.

  4. Supervised method to build an atlas database for multi-atlas segmentation-propagation

    NASA Astrophysics Data System (ADS)

    Shen, Kaikai; Bourgeat, Pierrick; Fripp, Jurgen; Mériaudeau, Fabrice; Ames, David; Ellis, Kathryn A.; Masters, Colin L.; Villemagne, Victor L.; Rowe, Christopher C.; Salvado, Olivier

    2010-03-01

    Multiatlas based segmentation-propagation approaches have been shown to obtain accurate parcelation of brain structures. However, this approach requires a large number of manually delineated atlases, which are often not available. We propose a supervised method to build a population specific atlas database, using the publicly available Internet Brain Segmentation Repository (IBSR). The set of atlases grows iteratively as new atlases are added, so that its segmentation capability may be enhanced in the multiatlas based approach. Using a dataset of 210 MR images of elderly subjects (170 elderly control, 40 Alzheimer's disease) from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study, 40 MR images were segmented to build a population specific atlas database for the purpose of multiatlas segmentation-propagation. The population specific atlases were used to segment the elderly population of 210 MR images, and were evaluated in terms of the agreement among the propagated labels. The agreement was measured by using the entropy H of the probability image produced when fused by voting rule and the partial moment μ2 of the histogram. Compared with using IBSR atlases, the population specific atlases obtained a higher agreement when dealing with images of elderly subjects.

  5. Gold(I)-catalysed synthesis of cyclic sulfamidates by intramolecular allene hydroamination.

    PubMed

    Higginbotham, Mari C M; Bebbington, Magnus W P

    2012-08-07

    Six-membered cyclic sulfamidates are prepared in high yields by treatment of allenic sulfamates with readily available gold(I) complexes. The reaction enables formation of N-substituted quaternary centres and complements existing processes for sulfamidate formation.

  6. Meniscus root refixation technique using a modified Mason-Allen stitch.

    PubMed

    Lee, Dhong Won; Jang, Suk Hwan; Ha, Jeong Ku; Kim, Jin Goo; Ahn, Jin Hwan

    2013-03-01

    A complete posterior medial meniscus root tear results in the inability to withstand hoop stress and requires the repair of the posterior medial meniscus root. Several techniques to repair the posterior medial meniscus root have been proposed, but most techniques are based on simple stitching. A modified Mason-Allen technique, recognized as a superior stitching method to repair rotator cuff in shoulder surgery, was applied to overcome the potential weakness of those simple stitching techniques. This newly modified Mason-Allen technique reproduces the locking effect of a conventional modified Mason-Allen stitch allowing the physiological meniscal extrusion. The purpose of this article is to describe a posterior root repair technique using a modified Mason-Allen stitch with two strands consisting of a simple horizontal and a simple vertical stitch. Level of evidence V.

  7. [Book review] Green engineering: environmentally conscious design, by David T. Allen and David R. Shonnard

    USGS Publications Warehouse

    Boustany, R.G.

    2002-01-01

    Review of: Green engineering: Environmentally conscious design / David T. Allen and David R. Shonnard / Prentice-Hall, Inc., One Lake Street, Upper Saddle River, NJ 07458. 2002. 552 pages. ISBN 0-13-061908-6.

  8. Wave acceleration of electrons in the Van Allen radiation belts.

    PubMed

    Horne, Richard B; Thorne, Richard M; Shprits, Yuri Y; Meredith, Nigel P; Glauert, Sarah A; Smith, Andy J; Kanekal, Shrikanth G; Baker, Daniel N; Engebretson, Mark J; Posch, Jennifer L; Spasojevic, Maria; Inan, Umran S; Pickett, Jolene S; Decreau, Pierrette M E

    2005-09-08

    The Van Allen radiation belts are two regions encircling the Earth in which energetic charged particles are trapped inside the Earth's magnetic field. Their properties vary according to solar activity and they represent a hazard to satellites and humans in space. An important challenge has been to explain how the charged particles within these belts are accelerated to very high energies of several million electron volts. Here we show, on the basis of the analysis of a rare event where the outer radiation belt was depleted and then re-formed closer to the Earth, that the long established theory of acceleration by radial diffusion is inadequate; the electrons are accelerated more effectively by electromagnetic waves at frequencies of a few kilohertz. Wave acceleration can increase the electron flux by more than three orders of magnitude over the observed timescale of one to two days, more than sufficient to explain the new radiation belt. Wave acceleration could also be important for Jupiter, Saturn and other astrophysical objects with magnetic fields.

  9. THE ALLEN TELESCOPE ARRAY SEARCH FOR ELECTROSTATIC DISCHARGES ON MARS

    SciTech Connect

    Anderson, Marin M.; Siemion, Andrew P. V.; Bower, Geoffrey C.; De Pater, Imke; Barott, William C.; Delory, Gregory T.; Werthimer, Dan

    2012-01-01

    The Allen Telescope Array was used to monitor Mars between 2010 March 9 and June 2, over a total of approximately 30 hr, for radio emission indicative of electrostatic discharge. The search was motivated by the report from Ruf et al. of the detection of non-thermal microwave radiation from Mars characterized by peaks in the power spectrum of the kurtosis, or kurtstrum, at 10 Hz, coinciding with a large dust storm event on 2006 June 8. For these observations, we developed a wideband signal processor at the Center for Astronomy Signal Processing and Electronics Research. This 1024 channel spectrometer calculates the accumulated power and power-squared, from which the spectral kurtosis is calculated post-observation. Variations in the kurtosis are indicative of non-Gaussianity in the signal, which can be used to detect variable cosmic signals as well as radio frequency interference (RFI). During the three-month period of observations, dust activity occurred on Mars in the form of small-scale dust storms; however, no signals indicating lightning discharge were detected. Frequent signals in the kurtstrum that contain spectral peaks with an approximate 10 Hz fundamental were seen at both 3.2 and 8.0 GHz, but were the result of narrowband RFI with harmonics spread over a broad frequency range.

  10. Ion nose spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

    2016-12-01

    We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  11. SETI Observations of Exoplanets with the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Harp, G. R.; Richards, Jon; Tarter, Jill C.; Dreher, John; Jordan, Jane; Shostak, Seth; Smolek, Ken; Kilsdonk, Tom; Wilcox, Bethany R.; Wimberly, M. K. R.; Ross, John; Barott, W. C.; Ackermann, R. F.; Blair, Samantha

    2016-12-01

    We report radio SETI observations on a large number of known exoplanets and other nearby star systems using the Allen Telescope Array (ATA). Observations were made over about 19000 hr from 2009 May to 2015 December. This search focused on narrowband radio signals from a set totaling 9293 stars, including 2015 exoplanet stars and Kepler objects of interest and an additional 65 whose planets may be close to their habitable zones. The ATA observations were made using multiple synthesized beams and an anticoincidence filter to help identify terrestrial radio interference. Stars were observed over frequencies from 1 to 9 GHz in multiple bands that avoid strong terrestrial communication frequencies. Data were processed in near-real time for narrowband (0.7-100 Hz) continuous and pulsed signals with transmitter/receiver relative accelerations from -0.3 to 0.3 m s-2. A total of 1.9 × 108 unique signals requiring immediate follow-up were detected in observations covering more than 8 × 106 star-MHz. We detected no persistent signals from extraterrestrial technology exceeding our frequency-dependent sensitivity threshold of 180-310 × 10-26 W m-2.

  12. Active and passive microwave measurements in Hurricane Allen

    NASA Technical Reports Server (NTRS)

    Delnore, V. E.; Bahn, G. S.; Grantham, W. L.; Harrington, R. F.; Jones, W. L.

    1985-01-01

    The NASA Langley Research Center analysis of the airborne microwave remote sensing measurements of Hurricane Allen obtained on August 5 and 8, 1980 is summarized. The instruments were the C-band stepped frequency microwave radiometer and the Ku-band airborne microwave scatterometer. They were carried aboard a NOAA aircraft making storm penetrations at an altitude of 3000 m and are sensitive to rain rate, surface wind speed, and surface wind vector. The wind speed is calculated from the increase in antenna brightness temperature above the estimated calm sea value. The rain rate is obtained from the difference between antenna temperature increases measured at two frequencies, and wind vector is determined from the sea surface normalized radar cross section measured at several azimuths. Comparison wind data were provided from the inertial navigation systems aboard both the C-130 aircraft at 3000 m and a second NOAA aircraft (a P-3) operating between 500 and 1500 m. Comparison rain rate data were obtained with a rain radar aboard the P-3. Evaluation of the surface winds obtained with the two microwave instruments was limited to comparisons with each other and with the flight level winds. Two important conclusions are drawn from these comparisons: (1) the radiometer is accurate when predicting flight level wind speeds and rain; and (2) the scatterometer produces well behaved and consistent wind vectors for the rain free periods.

  13. STS-46 Pilot Allen uses cycle ergometer on OV-104's middeck

    NASA Technical Reports Server (NTRS)

    1992-01-01

    STS-46 Pilot Andrew M. Allen exercises using the cycle ergometer on the middeck of Atlantis, Orbiter Vehicle (OV) 104. Allen, shirtless, is equipped with sensors for monitoring his biological systems during the exercise session. A communications kit assembly cable freefloats from his headset at his right and in front of the forward lockers. The open airlock hatch appears at his left and the sleep station behind him.

  14. Astronauts Gardner and Allen bringing Westar VI satellite into payload bay

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Dale A. Gardner, left, and Joseph P. Allen IV work together with Dr. Anna L. Fisher (in the Discovery controlling the remote manipulator system (RMS) arm) to bring the Westar VI satellite into the Discovery's payload bay. Allen is on a mobile foot restraint, which is attached to the RMS end effector. Gardner uses the manned maneuvering unit (MMU) on the other side of the satellite. He is attempting to remove the stinger device from the now stabilized satellite.

  15. Enantioselective Terminal Addition to Allenes by Dual Chiral Primary Amine/Palladium Catalysis.

    PubMed

    Zhou, Han; Wang, Yaning; Zhang, Long; Cai, Mao; Luo, Sanzhong

    2017-03-15

    We herein describe a synergistic chiral primary amine/achiral palladium catalyzed enantioselective terminal addition to allenes with α-branched β-ketocarbonyls and aldehydes. The reactions afford allylic adducts bearing acyclic all-carbon quaternary centers with high regio- and enantioselectivity. A wide range of allenes including those aliphatic or 1,1'-disubstituted could be employed, thus expanding the scope of typical asymmetric allylic alkylation reactions.

  16. Microwave-promoted synthesis of bicyclic azocine-β-lactams from bis(allenes).

    PubMed

    Alcaide, Benito; Almendros, Pedro; Aragoncillo, Cristina; Fernández, Israel; Gómez-Campillos, Gonzalo

    2014-08-01

    A metal-free preparation of structurally novel bicyclic azocine-β-lactams has been developed. The first examples accounting for the preparation of eight-membered rings from bis(allenes) in the absence of metals have been achieved by the thermolysis of nonconjugated 2-azetidinone-tethered bis(allenes) on application of microwave irradiation. This selective carbocyclization reaction has been studied experimentally, and additionally, its mechanism has been investigated by a DFT study.

  17. STS-46 Pilot Allen, in LES, at pilots station on OV-104's forward flight deck

    NASA Technical Reports Server (NTRS)

    1992-01-01

    STS-46 Pilot Andrew M. Allen, wearing launch and entry suit (LES) and launch and entry helmet (LEH), reviews descent procedural checklists while at pilots station on the forward flight deck of Atlantis, Orbiter Vehicle (OV) 104. The head-up display (HUD), flight mirror assembly, and forward windows appear in front of Allen. Control panels with drinking water containers and checklists are seen overhead.

  18. Geographical variation in bill size across bird species provides evidence for Allen's rule.

    PubMed

    Symonds, Matthew R E; Tattersall, Glenn J

    2010-08-01

    Allen's rule proposes that the appendages of endotherms are smaller, relative to body size, in colder climates, in order to reduce heat loss. Empirical support for Allen's rule is mainly derived from occasional reports of geographical clines in extremity size of individual species. Interspecific evidence is restricted to two studies of leg proportions in seabirds and shorebirds. We used phylogenetic comparative analyses of 214 bird species to examine whether bird bills, significant sites of heat exchange, conform to Allen's rule. The species comprised eight diverse taxonomic groups-toucans, African barbets, Australian parrots, estrildid finches, Canadian galliforms, penguins, gulls, and terns. Across all species, there were strongly significant relationships between bill length and both latitude and environmental temperature, with species in colder climates having significantly shorter bills. Patterns supporting Allen's rule in relation to latitudinal or altitudinal distribution held within all groups except the finches. Evidence for a direct association with temperature was found within four groups (parrots, galliforms, penguins, and gulls). Support for Allen's rule in leg elements was weaker, suggesting that bird bills may be more susceptible to thermoregulatory constraints generally. Our results provide the strongest comparative support yet published for Allen's rule and demonstrate that thermoregulation has been an important factor in shaping the evolution of bird bills.

  19. The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

    PubMed

    Nowinski, Wieslaw L; Belov, Dmitry

    2003-09-01

    The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

  20. Temperature of the plasmasphere from Van Allen Probes HOPE

    NASA Astrophysics Data System (ADS)

    Genestreti, K. J.; Goldstein, J.; Corley, G. D.; Farner, W.; Kistler, L. M.; Larsen, B. A.; Mouikis, C. G.; Ramnarace, C.; Skoug, R. M.; Turner, N. E.

    2017-01-01

    We introduce two novel techniques for estimating temperatures of very low energy space plasmas using, primarily, in situ data from an electrostatic analyzer mounted on a charged and moving spacecraft. The techniques are used to estimate proton temperatures during intervals where the bulk of the ion plasma is well below the energy bandpass of the analyzer. Both techniques assume that the plasma may be described by a one-dimensional E→×B→ drifting Maxwellian and that the potential field and motion of the spacecraft may be accounted for in the simplest possible manner, i.e., by a linear shift of coordinates. The first technique involves the application of a constrained theoretical fit to a measured distribution function. The second technique involves the comparison of total and partial-energy number densities. Both techniques are applied to Van Allen Probes Helium, Oxygen, Proton, and Electron (HOPE) observations of the proton component of the plasmasphere during two orbits on 15 January 2013. We find that the temperatures calculated from these two order-of-magnitude-type techniques are in good agreement with typical ranges of the plasmaspheric temperature calculated using retarding potential analyzer-based measurements - generally between 0.2 and 2 eV (2000-20,000 K). We also find that the temperature is correlated with L shell and hot plasma density and is negatively correlated with the cold plasma density. We posit that the latter of these three relationships may be indicative of collisional or wave-driven heating of the plasmasphere in the ring current overlap region. We note that these techniques may be easily applied to similar data sets or used for a variety of purposes.

  1. Ion nose spectral structures observed by the Van Allen Probes

    DOE PAGES

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

  2. Ion nose spectral structures observed by the Van Allen Probes

    SciTech Connect

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; Kistler, L. M.; Larsen, Brian Arthur; Reeves, Geoffrey D.; Skoug, Ruth M.; Funsten, Herbert O.

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  3. 76 FR 36318 - Safety Zone; Waterway Closure, Morgan City-Port Allen Route From Mile Marker 0 to Port Allen Lock

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-22

    ... and tows from destruction, loss or injury due to hazards associated with rising flood water. DATES... the general public, levee system, vessels and tows from the hazards associated with rising flood water... hazards associated with rising flood water on the Morgan City-Port Allen Route. Basis and Purpose...

  4. Clinical Evaluation of Zero-Echo-Time Attenuation Correction for Brain 18F-FDG PET/MRI: Comparison with Atlas Attenuation Correction.

    PubMed

    Sekine, Tetsuro; Ter Voert, Edwin E G W; Warnock, Geoffrey; Buck, Alfred; Huellner, Martin; Veit-Haibach, Patrick; Delso, Gaspar

    2016-12-01

    Accurate attenuation correction (AC) on PET/MR is still challenging. The purpose of this study was to evaluate the clinical feasibility of AC based on fast zero-echo-time (ZTE) MRI by comparing it with the default atlas-based AC on a clinical PET/MR scanner.

  5. The Open Anatomy Browser: A Collaborative Web-Based Viewer for Interoperable Anatomy Atlases

    PubMed Central

    Halle, Michael; Demeusy, Valentin; Kikinis, Ron

    2017-01-01

    The Open Anatomy Browser (OABrowser) is an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The viewer includes novel collaborative tools: users can save bookmarks of atlas views for later access and exchange those bookmarks with other users, and dynamic shared views allow groups of users can participate in a collaborative interactive atlas viewing session. We have published several anatomy atlases (an MRI-derived brain atlas and atlases of other parts of the anatomy) to demonstrate OABrowser’s functionality. The atlas source data, processing tools, and the source for OABrowser are freely available through GitHub and are distributed under a liberal open source license.

  6. The Open Anatomy Browser: A Collaborative Web-Based Viewer for Interoperable Anatomy Atlases.

    PubMed

    Halle, Michael; Demeusy, Valentin; Kikinis, Ron

    2017-01-01

    The Open Anatomy Browser (OABrowser) is an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The viewer includes novel collaborative tools: users can save bookmarks of atlas views for later access and exchange those bookmarks with other users, and dynamic shared views allow groups of users can participate in a collaborative interactive atlas viewing session. We have published several anatomy atlases (an MRI-derived brain atlas and atlases of other parts of the anatomy) to demonstrate OABrowser's functionality. The atlas source data, processing tools, and the source for OABrowser are freely available through GitHub and are distributed under a liberal open source license.

  7. A Tool for Brain-Wide Quantitative Analysis of Molecular Data upon Projection into a Planar View of Choice

    PubMed Central

    Vreysen, Samme; Scheyltjens, Isabelle; Laramée, Marie-Eve; Arckens, Lutgarde

    2017-01-01

    Several techniques, allowing the reconstruction and visualization of functional, anatomical or molecular information from tissue and organ slices, have been developed over the years. Yet none allow direct comparison without reprocessing the same slices. Alternative methods using publicly available reference maps like the Allen Brain Atlas lack flexibility with respect to age and species. We propose a new approach to reconstruct a segmented region of interest from serial slices by projecting the optical density values representing a given molecular signal to a plane of view of choice, and to generalize the results into a reference map, which is built from the individual maps of all animals under study. Furthermore, to allow quantitative comparison between experimental conditions, a non-parametric pseudo t-test has been implemented. This new mapping tool was applied, optimized and validated making use of an in situ hybridization dataset that represents the spatiotemporal expression changes for the neuronal activity reporter gene zif268, in relation to cortical plasticity induced by monocular enucleation, covering the entire mouse visual cortex. The created top view maps of the mouse brain allow precisely delineating and interpreting 11 extrastriate areas surrounding mouse V1. As such, and because of the opportunity to create a planar projection of choice, these molecular maps can in the future easily be compared with functional or physiological imaging maps created with other techniques such as Ca2+, flavoprotein and optical imaging. PMID:28144216

  8. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

    PubMed Central

    Krienen, Fenna M.; Yeo, B. T. Thomas; Ge, Tian; Buckner, Randy L.; Sherwood, Chet C.

    2016-01-01

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute’s human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections. PMID:26739559

  9. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    PubMed

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

  10. Effects of registration regularization and atlas sharpness on segmentation accuracy.

    PubMed

    Yeo, B T Thomas; Sabuncu, Mert R; Desikan, Rahul; Fischl, Bruce; Golland, Polina

    2008-10-01

    In non-rigid registration, the tradeoff between warp regularization and image fidelity is typically determined empirically. In atlas-based segmentation, this leads to a probabilistic atlas of arbitrary sharpness: weak regularization results in well-aligned training images and a sharp atlas; strong regularization yields a "blurry" atlas. In this paper, we employ a generative model for the joint registration and segmentation of images. The atlas construction process arises naturally as estimation of the model parameters. This framework allows the computation of unbiased atlases from manually labeled data at various degrees of "sharpness", as well as the joint registration and segmentation of a novel brain in a consistent manner. We study the effects of the tradeoff of atlas sharpness and warp smoothness in the context of cortical surface parcellation. This is an important question because of the increasingly availability of atlases in public databases, and the development of registration algorithms separate from the atlas construction process. We find that the optimal segmentation (parcellation) corresponds to a unique balance of atlas sharpness and warp regularization, yielding statistically significant improvements over the FreeSurfer parcellation algorithm. Furthermore, we conclude that one can simply use a single atlas computed at an optimal sharpness for the registration-segmentation of a new subject with a pre-determined, fixed, optimal warp constraint. The optimal atlas sharpness and warp smoothness can be determined by probing the segmentation performance on available training data. Our experiments also suggest that segmentation accuracy is tolerant up to a small mismatch between atlas sharpness and warp smoothness.

  11. Conjugate observations of quasiperiodic emissions by the Cluster, Van Allen Probes, and THEMIS spacecraft

    NASA Astrophysics Data System (ADS)

    Němec, F.; Hospodarsky, G.; Pickett, J. S.; Santolík, O.; Kurth, W. S.; Kletzing, C.

    2016-08-01

    We present results of a detailed analysis of two electromagnetic wave events observed in the inner magnetosphere at frequencies of a few kilohertz, which exhibit a quasiperiodic (QP) time modulation of the wave intensity. The events were observed by the Cluster and Van Allen Probes spacecraft and in one event also by the THEMIS E spacecraft. The spacecraft were significantly separated in magnetic local time, demonstrating a huge azimuthal extent of the events. Geomagnetic conditions at the times of the observations were very quiet, and the events occurred inside the plasmasphere. The modulation period observed by the Van Allen Probes and THEMIS E spacecraft (duskside) was in both events about twice larger than the modulation period observed by the Cluster spacecraft (dawnside). Moreover, individual QP elements occur about 15 s earlier on THEMIS E than on Van Allen Probes, which might be related to a finite propagation speed of a modulating ULF wave.

  12. Recent Results from the Relativistic Electron Proton Telescope (REPT) onboard the Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Kanekal, S. G.; Baker, D. N.; Elkington, S. R.; Hoxie, V. C.; Li, X.; Spence, H. E.

    2013-05-01

    We describe recent results from the REPT instruments on board Van Allen Probes mission launched on 30 August 2012. The twin spacecraft comprising the Van Allen probes mission are identically instrumented and carry a comprehensive suite of sensors characterizing magnetospheric charged particle populations, electric and magnetic fields and plasma waves. The REPT instruments comprise a well-shielded silicon solid state detector stack, with a state of the art electronics and measure electrons of ~1.5 to > 20 MeV and protons of ~17 to > 100 MeV. The instruments were commissioned 3 days after launch and continue to provide high quality measurements. We describe the Van Allen probes and the REPT instrument and report on the new and unexpected features of the outer zone electron populations observed by REPT.

  13. Space Weather data processing and Science Gateway for the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2013-12-01

    A near real-time data processing pipeline for the Space Weather broadcast data from the Van Allen Probes is presented. The Van Allen Probes broadcasts a sub-set of the science data in real-time when not downlinking the principal science data. This broadcast is received by several ground stations and relayed to APL in near real time to be ingested into the space weather processing pipeline. This pipeline processes the available level zero space weather data into higher level science data products. These products are made available to the public via the Van Allen Probes Science Gateway website (http://athena.jhuapl.edu). The website acts as pivotal point though which all other instrument SOC's can be accessed. Several other data products (e.g KP/DST indices) and tools (e.g orbit calculator) are made also available to the general public.

  14. An interspecific test of allen's rule: evolutionary implications for endothermic species.

    PubMed

    Nudds, R L; Oswald, S A

    2007-12-01

    Ecogeographical rules provide potential to describe how organisms are morphologically constrained to climatic conditions. Allen's rule (relatively shorter appendages in colder environments) remains largely unsupported and there remains much controversy whether reduced surface area of appendages provides energetic savings sufficient to make this morphological trend truly adaptive. By showing for the first time that Allen's rule holds for closely related endothermic species, we provide persuasive support of the adaptive significance of this trend for multiple species. Our results indicate that reduction of thermoregulatory cost during the coldest part of the breeding season is the most likely mechanism driving Allen's rule for these species. Because for 54% of seabird species examined, rise in seasonal maximum temperature over 100 years will exceed that for minimum temperatures, an evolutionary mismatch will arise between selection for limb length reduction and ability to accommodate heat stress.

  15. A Century after Van Allen's Birth: Conclusion of Reconnaissance of Radiation Belts in the Solar System

    NASA Astrophysics Data System (ADS)

    Krimigis, S. M.

    2014-12-01

    On May 1, 1958 in the Great Hall of the US National Academy of Sciences, James A. Van Allen, having instrumented Explorer-1 and follow-on satellites with radiation detectors, announced the discovery of intense radiation at high altitudes above Earth. The press dubbed the doughnut-shaped structures "Van Allen Belts" (VAB). Soon thereafter, the search began for VAB at nearby planets. Mariner 2 flew by Venus in 1962 at a distance of 41,000 km, but no radiation was detected. The Mariner 4 mission to Mars did not observe planet-associated increase in radiation, but scaling arguments with Earth's magnetosphere yielded an upper limit to the ratio of magnetic moments of MM/ME < 0.001 (Van Allen et al, 1965). Similarly, the Mariner 5 flyby closer to Venus resulted in a ratio of magnetic moments < 0.001 (Van Allen et al, 1967), dealing a blow to the expectation that all planetary bodies must possess significant VAB. The flyby of Mercury in 1974 by Mariner 10 revealed a weak magnetic field, but the presence of durably trapped higher energy particles remained controversial until MESSENGER in 2011.The first flybys of Jupiter by Pioneers 10, 11 in 1973 and 1974, respectively, measured a plethora of energetic particles in Jupiter's magnetosphere and established the fact that their intensities were rotationally modulated. Later flybys of Jupiter and Saturn by the two Voyagers in 1979 and 1981 revealed that those magnetospheres possessed their own internal plasma source(s) and radiation belts. Subsequent discoveries of Van Allen belts at Uranus and Neptune by Voyager 2 demonstrated that VAB are the rule rather than the exception in planetary environments. We now know from the Voyagers and through Energetic Neutral Atom images from Cassini and IBEX that an immense energetic particle population surrounds the heliosphere itself. Thus, the reconnaissance of radiation belts of our solar system has been completed, some 56 years after the discovery of the Van Allen Belts at Earth.

  16. MRI atlas of the brain

    SciTech Connect

    Bradley, W.G. ); Bydder, G. )

    1990-01-01

    Since most radiologists will start from a basic of familiarity with pathophysiology of disease and a knowledge of cross-sectional imaging (at least in the transaxial plane), they are in a good position to recognize and diagnose many of the abnormalities we can currently see with CT. The appearance of these lesions on MRI is the basis for the majority of the images in this book. Chapters on Tumors, Infarcts and Ischemia, Demyelination and Infection. Hydrocephalus, and Pediatrics feature multiple images displaying the MR appearance of many common lesions with minimal associated text. Instead of focusing on pathophysiology, attention is directed to the variable appearance of these disease states using various MR imaging techniques. Although the MR contrast agent, Gadolinium-DTPA, has similar behavior (physiologically) to meglumine diatrizoate in CT, the MR techniques which result in optimal visualization of enhancing lesions are nonintuitive and are discussed. Similarly, the appearance of flowing blood and CSF and hemorrhage does not follow easily from a pre-existing CT base, therefore additional text has been devoted to these subjects.

  17. View-centralized multi-atlas classification for Alzheimer's disease diagnosis.

    PubMed

    Liu, Mingxia; Zhang, Daoqiang; Shen, Dinggang

    2015-05-01

    Multi-atlas based methods have been recently used for classification of Alzheimer's disease (AD) and its prodromal stage, that is, mild cognitive impairment (MCI). Compared with traditional single-atlas based methods, multiatlas based methods adopt multiple predefined atlases and thus are less biased by a certain atlas. However, most existing multiatlas based methods simply average or concatenate the features from multiple atlases, which may ignore the potentially important diagnosis information related to the anatomical differences among different atlases. In this paper, we propose a novel view (i.e., atlas) centralized multi-atlas classification method, which can better exploit useful information in multiple feature representations from different atlases. Specifically, all brain images are registered onto multiple atlases individually, to extract feature representations in each atlas space. Then, the proposed view-centralized multi-atlas feature selection method is used to select the most discriminative features from each atlas with extra guidance from other atlases. Next, we design a support vector machine (SVM) classifier using the selected features in each atlas space. Finally, we combine multiple SVM classifiers for multiple atlases through a classifier ensemble strategy for making a final decision. We have evaluated our method on 459 subjects [including 97 AD, 117 progressive MCI (p-MCI), 117 stable MCI (s-MCI), and 128 normal controls (NC)] from the Alzheimer's Disease Neuroimaging Initiative database, and achieved an accuracy of 92.51% for AD versus NC classification and an accuracy of 78.88% for p-MCI versus s-MCI classification. These results demonstrate that the proposed method can significantly outperform the previous multi-atlas based classification methods.

  18. Experiments in no-impact control of dingoes: comment on Allen et al. 2013.

    PubMed

    Johnson, Christopher N; Crowther, Mathew S; Dickman, Chris R; Letnic, Michael I; Newsome, Thomas M; Nimmo, Dale G; Ritchie, Euan G; Wallach, Arian D

    2014-02-22

    There has been much recent debate in Australia over whether lethal control of dingoes incurs environmental costs, particularly by allowing increase of populations of mesopredators such as red foxes and feral cats. Allen et al. (2013) claim to show in their recent study that suppression of dingo activity by poison baiting does not lead to mesopredator release, because mesopredators are also suppressed by poisoning. We show that this claim is not supported by the data and analysis reported in Allen et al.'s paper.

  19. Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

    PubMed

    Sooman, Linda; Wennman, Anneli; Hamberg, Mats; Hoffmann, Inga; Oliw, Ernst H

    2016-02-01

    The genome of Aspergillus niger codes for a fusion protein (EHA25900), which can be aligned with ~50% sequence identity to 9S-dioxygenase (DOX)-allene oxide synthase (AOS) of Fusarium oxysporum, homologues of the Fusarium and Colletotrichum complexes and with over 62% sequence identity to homologues of Aspergilli, including (DOX)-9R-AOS of Aspergillus terreus. The aims were to characterize the enzymatic activities of EHA25900 and to identify crucial amino acids for the stereospecificity. Recombinant EHA25900 oxidized 18:2n-6 sequentially to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE) and to a 9R(10)-allene oxide. 9S- and 9R-DOX-AOS catalyze abstraction of the pro-R hydrogen at C-11, but the direction of oxygen insertion differs. A comparison between twelve 9-DOX domains of 9S- and 9R-DOX-AOS revealed conserved amino acid differences, which could contribute to the chirality of products. The Gly616Ile replacement of 9R-DOX-AOS (A. niger) increased the biosynthesis of 9S-HPODE and the 9S(10)-allene oxide, whereas the Phe627Leu replacement led to biosynthesis of 9S-HPODE and the 9S(10)-allene oxide as main products. The double mutant (Gly616Ile, Phe627Leu) formed over 90% of the 9S stereoisomer of HPODE. 9S-HPODE was formed by antarafacial hydrogen abstraction and oxygen insertion, i.e., the original H-abstraction was retained but the product chirality was altered. We conclude that 9R-DOX-AOS can be altered to 9S-DOX-AOS by replacement of two amino acids (Gly616Ile, Phe627Leu) in the DOX domain.

  20. Regioselective Allene Hydrosilylation Catalyzed by NHC Complexes of Nickel and Palladium

    PubMed Central

    Miller, Zachary D.; Li, Wei; Belderrain, Tomás R.; Montgomery, John

    2013-01-01

    Regioselective methods for allene hydrosilylation have been developed, with regioselectivity being governed primarily by choice of metal. Alkenylsilanes are produced via nickel catalysis with larger N-heterocyclic carbene ligands, and allylsilanes are produced via palladium catalysis with smaller N-heterocyclic carbene ligands. These complementary methods allow either regioisomeric product to be obtained with exceptional regiocontrol. PMID:24079389

  1. Phosphorus-Containing Bis-allenes: Synthesis and Heterocyclization Reactions Mediated by Iodine or Copper Dibromide.

    PubMed

    Essid, I; Laborde, C; Legros, F; Sevrain, N; Touil, S; Rolland, M; Ayad, T; Volle, J-N; Pirat, J-L; Virieux, D

    2017-03-30

    Bisphosphorylallenes were easily obtained in multigram scale from the Wittig-type rearrangement of bispropargyl alcohols. Unlike other conjugated bis-allenes, these reagents underwent a double cyclization mediated by iodine or copper dibromide leading to the formation of bis-1,2-oxaphospholenes.

  2. No Radio Flaring Detected from Cygnus X-3 at 3 GHz by Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Williams, P. K. G.; Bower, G. C.; Tomsick, J. A.; Bodaghee, A.; Corbet, R. H. D.

    2011-01-01

    Following the announcement of a 98 GHz flare from the microquasar Cygnus X-3 (ATel #3130), we observed it with the Allen Telescope Array (Welch et al., 2009 Proc. IEEE 97 1438 for 2.5 hours beginning at 2011 January 28.848 UT (MJD 55589.848), about 4.0 hours after the 98 GHz observations concluded.

  3. Astronauts Gardner and Allen on the RMS after recapture of Westar VI

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Dale A. Gardner, left, holds a 'For Sale' sign, making light reference to the status of the recaptured communications satellite. Astronaut Joseph P. ALlen IV stands on the mobile foot restraint (MFR), which in tandem with the remote manipulator system (RMS) arm served as a cherry-picker for capture efforts.

  4. Astronauts Gardner and Allen during loading of Palapa B-2 in payload bay

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen IV, left, tethered to the orbiting Discovery, holds onto the Palapa B-2 satellite with his right hand while Astronaut Dale A. Gardner returns the used 'stinger' device to its stowage area. The payload bay is open, showing the area where the satellite will be stowed for the return to Earth.

  5. All Together Now: Valerie Allen--U.S. Department of Energy

    ERIC Educational Resources Information Center

    Library Journal, 2005

    2005-01-01

    When Valerie Allen decided she did not want to be a Montessori teacher any longer, she began work on her MLIS. Immediately she learned concepts she could apply to her new job as information specialist for the Department of Energy's (DOE) Office of Scientific and Technical Information (OSTI) at Oak Ridge National Laboratory, TN. While the LIS…

  6. Free Pulp Transfer for Fingertip Reconstruction—The Algorithm for Complicated Allen Fingertip Defect

    PubMed Central

    Spyropoulou, Georgia-Alexandra; Shih, Hsiang-Shun

    2015-01-01

    Abstract Background: We present a review of all the cases of free toe pulp transfer and an algorithm for application of free pulp transfer in complicated Allen fingertip defect. Methods: Seventeen patients underwent free toe pulp transfer for fingertip reconstruction by the senior author. Twelve cases were Allen type II with oblique pulp defect, 4 were Allen type III, and 1 patient had 2 fingertip injuries classified both as type IV. According to the algorithm presented, for the type III defects where the germinal matrix is still preserved, we use free pulp transfer and nail bed graft to preserve the nail growth instead of toe to hand transfer. For the type IV injuries with multiple defects, a combination of web flap from both big toe and second toe is possible for 1-stage reconstruction. Results: All pulp flaps survived completely. Static 2-point discrimination ranged from 6 to 15 mm (mean: 10.5 mm). No patient presented dysesthesia, hyperesthesia, pain at rest, or cold intolerance. The donor site did not present any nuisances apart from partial skin graft loss in 3 cases. Conclusions: We tried to classify and modify the defects’ reconstruction according to Allen classification. Free toe pulp transfer is a “like with like” reconstruction that provides sensate, glabrous skin with good color and texture match for fingertip trauma, and minimal donor site morbidity compared with traditional toe to hand transfer. PMID:26894009

  7. Astronauts Joseph Allen rides cherry picker over stowage area/work station

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen rides a cherry picker over to a stowage area/work station to wrap up extravehicular activity (EVA) duties above Earth. The cherry picker is a union of the mobile foot restraint and the remote manipulator system (RMS), controlled from inside Discovery's cabin. The Westar VI/PAM-D satellite is pictured secured in Discovery's cargo bay.

  8. Precipitation of relativistic electrons of the Van Allen belts into the proton aurora

    SciTech Connect

    Jordanova, Vania K; Miyoshi, Y; Sakaguchi, K; Shiokawa, K; Evans, D S; Connors, M

    2008-01-01

    The Van Allen electron belts consist of two regions encircling the earth in which relativistic electrons are trapped in the earth's magnetic field. Populations of relativistic electrons in the Van Allen belts vary greatly with geomagnetic disturbance and they are a major source of damage to space vehicles. In order to know when and by how much these populations of relativistic electrons increase, it is important to elucidate not only the cause of acceleration of relativistic electrons but also the cause of their loss from the Van Allen belts. Here we show the first evidence that left-hand polarized electromagnetic ion cyclotron (EMIC) plasma waves can cause the loss of relativistic electrons into the atmosphere, on the basis of results of an excellent set of ground and satellite observations showing coincident precipitation of ions with energies of tens of keV and of relativistic electrons into an isolated proton aurora. The proton aurora was produced by precipitation of ions with energies of tens of keV due to EMIC waves near the plasma pause, which is a manifestation of wave-particle interactions. These observations clarify that ions with energies of tens of keV affect the evolution of relativistic electrons in the Van Allen belts via parasitic resonance with EMIC waves, an effect that was first theoretically predicted in the early 1970's.

  9. New Results About the Earth’s Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Baker, Daniel

    2015-01-01

    The first great scientific discovery of the Space Age was that the Earth is enshrouded in toroids, or 'belts', of very high-energy magnetically trapped charged particles. Early observations of the radiation environment clearly indicated that the Van Allen belts could be delineated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons in the energy range 100 keV < E< 1 MeV often populated both the inner and outer zones with a pronounced 'slot' region relatively devoid of energetic electrons existing between them. This two-belt structure for the Van Allen moderate-energy electron component was explained as being due to strong interactions of electrons with electromagnetic waves just inside the cold plasma (plasmapause) boundary. The energy distribution, spatial extent and particle species makeup of the Van Allen belts has been subsequently explored by several space missions. However, recent observations by the NASA dual-spacecraft Van Allen Probes mission have revealed wholly unexpected properties of the radiation belts, especially at highly relativistic (E > 2 MeV) and ultra-relativistic (E > 5 MeV) kinetic energies. In this presentation we show using high spatial and temporal resolution data from the Relativistic Electron-Proton Telescope (REPT) experiment on board the Van Allen Probes that multiple belts can exist concurrently and that an exceedingly sharp inner boundary exists for ultra-relativistic electrons. Using additionally available Van Allen Probes data, we demonstrate that these remarkable features of energetic electrons are not due to a physical boundary within Earth's intrinsic magnetic field. Neither is it likely that human-generated electromagnetic transmitter wave fields might produce such effects. Rather, we conclude from these unique measurements that slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle

  10. Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: Application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants.

    PubMed

    Akazawa, Kentaro; Chang, Linda; Yamakawa, Robyn; Hayama, Sara; Buchthal, Steven; Alicata, Daniel; Andres, Tamara; Castillo, Deborrah; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2016-03-01

    Diffusion tensor imaging (DTI) has been widely used to investigate the development of the neonatal and infant brain, and deviations related to various diseases or medical conditions like preterm birth. In this study, we created a probabilistic map of fiber pathways with known associated functions, on a published neonatal multimodal atlas. The pathways-of-interest include the superficial white matter (SWM) fibers just beneath the specific cytoarchitectonically defined cortical areas, which were difficult to evaluate with existing DTI analysis methods. The Jülich cytoarchitectonic atlas was applied to define cortical areas related to specific brain functions, and the Dynamic Programming (DP) method was applied to delineate the white matter pathways traversing through the SWM. Probabilistic maps were created for pathways related to motor, somatosensory, auditory, visual, and limbic functions, as well as major white matter tracts, such as the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle, by delineating these structures in eleven healthy term-born neonates. In order to characterize maturation-related changes in diffusivity measures of these pathways, the probabilistic maps were then applied to DTIs of 49 healthy infants who were longitudinally scanned at three time-points, approximately five weeks apart. First, we investigated the normal developmental pattern based on 19 term-born infants. Next, we analyzed 30 preterm-born infants to identify developmental patterns related to preterm birth. Last, we investigated the difference in diffusion measures between these groups to evaluate the effects of preterm birth on the development of these functional pathways. Term-born and preterm-born infants both demonstrated a time-dependent decrease in diffusivity, indicating postnatal maturation in these pathways, with laterality seen in the corticospinal tract and the optic radiation. The comparison between term- and preterm

  11. Unbiased atlas formation via large deformations metric mapping.

    PubMed

    Lorenzen, Peter; Davis, Brad; Joshi, Sarang

    2005-01-01

    The construction of population atlases is a key issue in medical image analysis, and particularly in brain mapping. Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and to facilitate tissue and object segmentation via registration of anatomical labels. We formulate the unbiased atlas construction problem as a Fréchet mean estimation in the space of diffeomorphisms via large deformations metric mapping. A novel method for computing constant speed velocity fields and an analysis of atlas stability and robustness using entropy are presented. We address the question: how many images are required to build a stable brain atlas?

  12. Enantioselective Synthesis of 5,7-Bicyclic Ring Systems from Axially Chiral Allenes Using a Rh(I)-Catalyzed Cyclocarbonylation Reaction

    PubMed Central

    Grillet, Francois; Brummond, Kay M.

    2013-01-01

    A transfer of chirality in an intramolecular Rh(I)-catalyzed allenic Pauson-Khand reaction (APKR) to access tetrahydroazulenones, tetrahydrocyclopenta[c]azepinones and dihydrocyclopenta[c]oxepinones enantioselectively (22 – 99% ee) is described. The substitution pattern of the allene affected the transfer of chiral information. Complete transfer of chirality was obtained for all trisubstituted allenes, but loss of chiral information was observed for disubstituted allenes. This work constitutes the first demonstration of a transfer of chiral information from an allene to the 5-position of a cyclopentenone using a cyclocarbonylation reaction. The absolute configuration of the corresponding cyclocarbonylation product was also established, something that is rarely done. PMID:23485149

  13. Steps towards automatic building of anatomical atlases

    NASA Astrophysics Data System (ADS)

    Subsol, Gerard; Thirion, Jean-Philippe; Ayache, Nicholas

    1994-09-01

    This paper presents a general scheme for the building of anatomical atlases. We propose to use specific and stable features, the crest lines (or ridge lines) which are automatically extracted from 3D images by differential geometry operators. We have developed non-rigid registration techniques based on polynomial transformations to find correspondences between lines. We got encouraging results for the building of atlases of the crest lines of the skull and of the brain based on several CT-Scan and MRI images of different patients.

  14. Revealing latent value of clinically acquired CTs of traumatic brain injury through multi-atlas segmentation in a retrospective study of 1,003 with external cross-validation

    NASA Astrophysics Data System (ADS)

    Plassard, Andrew J.; Kelly, Patrick D.; Asman, Andrew J.; Kang, Hakmook; Patel, Mayur B.; Landman, Bennett A.

    2015-03-01

    Medical imaging plays a key role in guiding treatment of traumatic brain injury (TBI) and for diagnosing intracranial hemorrhage; most commonly rapid computed tomography (CT) imaging is performed. Outcomes for patients with TBI are variable and difficult to predict upon hospital admission. Quantitative outcome scales (e.g., the Marshall classification) have been proposed to grade TBI severity on CT, but such measures have had relatively low value in staging patients by prognosis. Herein, we examine a cohort of 1,003 subjects admitted for TBI and imaged clinically to identify potential prognostic metrics using a "big data" paradigm. For all patients, a brain scan was segmented with multi-atlas labeling, and intensity/volume/texture features were computed in a localized manner. In a 10-fold crossvalidation approach, the explanatory value of the image-derived features is assessed for length of hospital stay (days), discharge disposition (five point scale from death to return home), and the Rancho Los Amigos functional outcome score (Rancho Score). Image-derived features increased the predictive R2 to 0.38 (from 0.18) for length of stay, to 0.51 (from 0.4) for discharge disposition, and to 0.31 (from 0.16) for Rancho Score (over models consisting only of non-imaging admission metrics, but including positive/negative radiological CT findings). This study demonstrates that high volume retrospective analysis of clinical imaging data can reveal imaging signatures with prognostic value. These targets are suited for follow-up validation and represent targets for future feature selection efforts. Moreover, the increase in prognostic value would improve staging for intervention assessment and provide more reliable guidance for patients.

  15. Revealing Latent Value of Clinically Acquired CTs of Traumatic Brain Injury Through Multi-Atlas Segmentation in a Retrospective Study of 1,003 with External Cross-Validation.

    PubMed

    Plassard, Andrew J; Kelly, Patrick D; Asman, Andrew J; Kang, Hakmook; Patel, Mayur B; Landman, Bennett A

    2015-03-20

    Medical imaging plays a key role in guiding treatment of traumatic brain injury (TBI) and for diagnosing intracranial hemorrhage; most commonly rapid computed tomography (CT) imaging is performed. Outcomes for patients with TBI are variable and difficult to predict upon hospital admission. Quantitative outcome scales (e.g., the Marshall classification) have been proposed to grade TBI severity on CT, but such measures have had relatively low value in staging patients by prognosis. Herein, we examine a cohort of 1,003 subjects admitted for TBI and imaged clinically to identify potential prognostic metrics using a "big data" paradigm. For all patients, a brain scan was segmented with multi-atlas labeling, and intensity/volume/texture features were computed in a localized manner. In a 10-fold cross-validation approach, the explanatory value of the image-derived features is assessed for length of hospital stay (days), discharge disposition (five point scale from death to return home), and the Rancho Los Amigos functional outcome score (Rancho Score). Image-derived features increased the predictive R(2) to 0.38 (from 0.18) for length of stay, to 0.51 (from 0.4) for discharge disposition, and to 0.31 (from 0.16) for Rancho Score (over models consisting only of non-imaging admission metrics, but including positive/negative radiological CT findings). This study demonstrates that high volume retrospective analysis of clinical imaging data can reveal imaging signatures with prognostic value. These targets are suited for follow-up validation and represent targets for future feature selection efforts. Moreover, the increase in prognostic value would improve staging for intervention assessment and provide more reliable guidance for patients.

  16. A stereotaxic atlas for the telencephalon of the Siamese fighting fish (Betta splendens).

    PubMed

    Marino-Neto, J; Sabbatini, R M

    1988-01-01

    1. A stereotaxic technique for electrode positioning in the telencephalic nuclei of the Siamese Fighting fish (Betta splendens) is described. 2. The forebrain atlas was based on paraffin-embedded, in situ-sectioned, Nissl-stained material. Brain measurements were corrected for tissue shrinkage due to histological procedures. The atlas and methods have already been tested and have shown good accuracy and reproducibility.

  17. Electron acceleration in the heart of the Van Allen radiation belts.

    PubMed

    Reeves, G D; Spence, H E; Henderson, M G; Morley, S K; Friedel, R H W; Funsten, H O; Baker, D N; Kanekal, S G; Blake, J B; Fennell, J F; Claudepierre, S G; Thorne, R M; Turner, D L; Kletzing, C A; Kurth, W S; Larsen, B A; Niehof, J T

    2013-08-30

    The Van Allen radiation belts contain ultrarelativistic electrons trapped in Earth's magnetic field. Since their discovery in 1958, a fundamental unanswered question has been how electrons can be accelerated to such high energies. Two classes of processes have been proposed: transport and acceleration of electrons from a source population located outside the radiation belts (radial acceleration) or acceleration of lower-energy electrons to relativistic energies in situ in the heart of the radiation belts (local acceleration). We report measurements from NASA's Van Allen Radiation Belt Storm Probes that clearly distinguish between the two types of acceleration. The observed radial profiles of phase space density are characteristic of local acceleration in the heart of the radiation belts and are inconsistent with a predominantly radial acceleration process.

  18. Automated determination of electron density from electric field measurements on the Van Allen Probes spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, Irina; Kurth, William; Spasojevic, Maria; Shprits, Yuri

    2016-07-01

    We present the Neural-network-based Upper-hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurements made onboard NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, f_{uhr}, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detections. We describe the design and implementation of the algorithm and perform an initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the EMFISIS instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.

  19. Cycloaddition reactions of allenes with N-phenylmaleimide. A two-step, diradical-intermediate process

    SciTech Connect

    Pasto, D.J.; Heid, P.F.; Warren, S.E.

    1982-06-30

    The stereoselectivities, chemoselectivities, relative reactivities, and kinetic isotope effects have been determined in the cycloaddition reactions of substituted allenes with N-phenylmaleimide. The comparison of these results with those derived from the studies of the cycloaddition of 1,1-dichloro-2,2-difluoroethene and the radical-chain addition of benzenethiol to allenes strongly indicates that the cycloadditions with N-phenylmaleimide occur via a two-step, diradical-intermediate process. The stereochemical features controlling the formation of the stereoisomeric diradical intermediates and their ring closures are discussed. In addition to the cycloaddition processes, competitive ene reactions occur to produce intermediate dienes, which react further to produce 1:2 adducts or nonreactive alkyne-containing 1:1 adducts. These ene reactions also appear to proceed via diradical intermediates.

  20. Ruthenium Catalyzed Reductive Coupling of Paraformaldehyde to Trifluoromethyl Allenes: CF3-Bearing All-Carbon Quaternary Centers

    PubMed Central

    Sam, Brannon; Montgomery, T. Patrick; Krische, Michael J.

    2013-01-01

    Trifluoromethyl substituted allenes engage in ruthenium catalyzed reductive couplings with paraformaldehyde to form products of hydrohydroxymethylation as single regioisomers. This method enables generation of CF3-bearing all-carbon quaternary stereocenters. PMID:23841678

  1. Enantioselective and Regiodivergent Addition of Purines to Terminal Allenes: Synthesis of Abacavir.

    PubMed

    Thieme, Niels; Breit, Bernhard

    2017-02-01

    The rhodium-catalyzed atom-economic asymmetric N-selective intermolecular addition of purine derivatives to terminal allenes is reported. Branched allylic purines were obtained in high yields, regioselectivity and outstanding enantioselectivity utilizing a Rh/Josiphos catalyst. Conversely, linear selective allylation of purines could be realized in good to excellent regio- and E/Z-selectivity with a Pd/dppf catalyst system. Furthermore, the new methodology was applied to a straightforward asymmetric synthesis of carbocyclic nucleoside abacavir.

  2. Van Allen Probes observations of electromagnetic ion cyclotron waves triggered by enhanced solar wind dynamic pressure

    NASA Astrophysics Data System (ADS)

    Cho, J.-H.; Lee, D.-Y.; Noh, S.-J.; Shin, D.-K.; Hwang, J.; Kim, K.-C.; Lee, J. J.; Choi, C. R.; Thaller, S.; Skoug, R.

    2016-10-01

    Magnetospheric compression due to impact of enhanced solar wind dynamic pressure Pdyn has long been considered as one of the generation mechanisms of electromagnetic ion cyclotron (EMIC) waves. With the Van Allen Probe-A observations, we identify three EMIC wave events that are triggered by Pdyn enhancements under prolonged northward interplanetary magnetic field (IMF) quiet time preconditions. They are in contrast to one another in a few aspects. Event 1 occurs in the middle of continuously increasing Pdyn while Van Allen Probe-A is located outside the plasmapause at postmidnight and near the equator (magnetic latitude (MLAT) -3°). Event 2 occurs by a sharp Pdyn pulse impact while Van Allen Probe-A is located inside the plasmapause in the dawn sector and rather away from the equator (MLAT 12°). Event 3 is characterized by amplification of a preexisting EMIC wave by a sharp Pdyn pulse impact while Van Allen Probe-A is located outside the plasmapause at noon and rather away from the equator (MLAT -15°). These three events represent various situations where EMIC waves can be triggered by Pdyn increases. Several common features are also found among the three events. (i) The strongest wave is found just above the He+ gyrofrequency. (ii) The waves are nearly linearly polarized with a rather oblique propagation direction ( 28° to 39° on average). (iii) The proton fluxes increase in immediate response to the Pdyn impact, most significantly in tens of keV energy, corresponding to the proton resonant energy. (iv) The temperature anisotropy with T⊥ > T|| is seen in the resonant energy for all the events, although its increase by the Pdyn impact is not necessarily always significant. The last two points (iii) and (iv) may imply that in addition to the temperature anisotropy, the increase of the resonant protons must have played a critical role in triggering the EMIC waves by the enhanced Pdyn impact.

  3. Astronauts Gardner and Allen during loading of Palapa B-2 in payload bay

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen, in this frame, is the sole anchor for the top portion (and most of) the captured Palapa B-2 satellite. Astronaut Dale A. Gardner is on the other end as they load it into the payload bay. Note the difference between the two stinger devices stowed on the Challenger's port side (right side of frame). The one nearer the spacecraft's vertical stabilizer is spent. The one nearer the camera is still awaiting use.

  4. Whistler-Mode Waves inside Density Ducts Observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Rosborough, S.; Bengtson, M.; Stein, R. L.; Streltsov, A. V.

    2015-12-01

    The Van Allen Probes satellites launched by NASA in 2012 are currently orbiting in Earth's radiation belts collecting data about electromagnetic waves and charged particles in the near-earth space environment. Whistler-mode waves are naturally occurring right-hand polarized, very-low frequency waves (< 30 kHz), that can efficiently interact with the energetic electrons in the earth's radiation belts magnetosphere and remediate them from the magnetosphere by precipitating these particles into the atmosphere. The important property of the whistler-mode waves is that they can be guided by density inhomogeneities extended along the ambient magnetic field and localized in the direction perpendicular to the field. Such density channels can be formed by the density enhancement or depletion and they are called ducts. The primary goal of our research is to find density duct and whistler waves in the data recorded by the Van Allen Probes satellites in the magnetosphere, and to reproduce these data with numerical simulations of time-dependent, two-dimensional electron MHD model. In this paper, we present results from our analysis of the observations performed by the Van Allen Probes satellites on 15 October 2014. Data from the probes show the electric and magnetic fields and plasma density. In this event whistler-mode waves were observed from 01:42 to 01:54 UT inside the localized density enhancement coincided with the flux of energetic electrons. Short time intervals, high concentrated electron density, and electron flux gradient activity make this event very interesting for the investigation. Numerical simulations of the electron MHD model revels reasonable quantitative agreement between numerical results and satellite observations, suggesting that the electromagnetic disturbances recorded by the Van Allen Probes satellites, are the whistler-mode waves indeed.

  5. Allene as the parent substrate in zinc-mediated biomimetic hydration reactions of cumulenes.

    PubMed

    Jahn, Burkhard O; Eger, Wilhelm A; Anders, Ernst

    2008-11-07

    The aim of our present investigation is to unravel the general mode of biomimetic activation of a wide variety of cumulenes by carbonic anhydrase (CA) models. Carbonic anhydrases allow the specific recognition, activation and transfer not only of CO2 but also of heteroallenes X=C=Y such as the polar or polarizable examples COS, CS2, H2CCO, and RNCS. Therefore, this enzyme class fulfils the requirements of excellent catalysts with a wide variety of important applications. Can this be extended to the isoelectronic but less reactive allene molecule, H2C=C=CH2 and extremely simplified models as mimetic concept for active center of the carbonic anhydrase? Allene is a waste product in the refinery, i.e. the C3-cut of the naphtha distillation; therefore, any addition product that can be obtained from allene in high yields will be of significant value. We investigated the complete catalytic cycle of a very simple model reaction, the hydration of allene, using density functional theory. Additionally, calculations were performed for the uncatalyzed reaction. There are two possible ways for the nucleophilic attack leading to different products. The zinc hydroxide complex and the water molecule can react at the central or the terminal carbon atoms (positional selectivity), the resulting products are 2-propen-1-ol and propen-2-ol, respectively, acetone. The calculations indicate a significant lower energy barrier for the rate determining step of the formation of propen-2-ol and therefore a well-expressed regioselectivity for the addition of such small molecules. The zinc complex has a pronounced catalytic effect and lowers the activation barrier from 262.5 to 123.9 kJ/mol compared with the uncatalyzed reaction. This work suggests the most probable paths for this reaction and discloses the necessity for the development of novel catalysts.

  6. Palladium-Catalyzed Formal (5 + 2) Annulation between ortho-Alkenylanilides and Allenes.

    PubMed

    Cendón, Borja; Casanova, Noelia; Comanescu, Cezar; García-Fandiño, Rebeca; Seoane, Andrés; Gulías, Moisés; Mascareñas, José L

    2017-04-07

    2-Alkenyltriflylanilides react with allenes upon treatment with catalytic amounts of Pd(OAc)2 and Cu(II) to give highly valuable 2,3-dihydro-1H-benzo[b]azepines, in good yields, and with very high regio- and diastereoselectivities. Density functional theory (DFT) calculations suggest that the C-H activation of the alkenylanilide involves a classical concerted metalation-deprotonation (CMD) mechanism.

  7. Nonlinear wave-particle interactions in the outer radiation belts: Van Allen Probes results

    NASA Astrophysics Data System (ADS)

    Agapitov, Oleksiy; Mozer, Forrest; Artemyev, Anton; Drake, James; Vasko, Ivan

    2016-10-01

    Huge numbers of different nonlinear structures (double layers, electron holes, non-linear whistlers, etc. referred to as Time Domain Structures - TDS) have been observed by the electric field experiment on board the Van Allen Probes. A large part of the observed non-linear structures are associated with whistler waves and some of them can be directly driven by whistlers. Observations of electron velocity distributions and chorus waves by the Van Allen Probe B provided long-lasting signatures of electron Landau resonant interactions with oblique chorus waves in the outer radiation belt. In the inhomogeneous geomagnetic field, such resonant interactions then lead to the formation of a plateau in the parallel (with respect to the geomagnetic field) velocity distribution due to trapping of electrons into the wave effective potential. The feedback from trapped particles provides steepening of parallel electric field and development of TDS seeded from initial whistler structure (well explained in terms of Particle-In-Cell model). The decoupling of the whistler wave and the nonlinear electrostatic component is shown in PIC simulation in the inhomogeneous magnetic field system and are observed by the Van Allen Probes in the radiation belts.

  8. Observation of plasma depletions in outer radiation belt by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Lee, J.; Kim, K.; Lee, E.; Kim, Y.; Park, Y.; Parks, G. K.; Sibeck, D. G.

    2013-12-01

    Van Allen Probes (RBSP) observed plasma fine structures in the outer radiation belt during storm time on 14 November 2012. Five plasma depletion regions are clearly identified by VAP_A and VAP_B from 02:00UT to 04:45UT by particle instrument suite that can measure electrons and ions in a wide energy range, from 20 eV to 10 MeV. The plasma flux density dramatically decreases about 2 - 3 orders of magnitude in the depletion regions regardless of energy and particle species. Our analysis shows the plasma cavities are formed at the boundary of trapped and injected particle current. The total plasma pressures inside the depletion regions are much smaller than outside, implying unstable structures. It seems that this structures appear unusually only for storm main phase. During strong storm event, geomagnetic field is stretched and low plasma density region (lobe) moves to low latitude, this event could be analyzed by lobe region crossing of spacecraft. However, to explain temporal sequences of this event, we should assume large fluctuation of lobe boundary. Another possible analysis is plasma bubble generated in the tail region. The bubble model proposed to explain plasma transportation form tail to near Earth region in 1980s. While the bubble model reasonably explain the spatial and temporal structures observed by Van Allen probes, we cannot completely rule out the lobe region crossing model. In this presentation, we shall discuss about the characteristics of the plasma density cavities first observed by Van Allen Probes.

  9. Radition belt dynamics : Recent results from van Allen Probes and future observations from CeREs

    NASA Astrophysics Data System (ADS)

    Kanekal, Shrikanth; O'Brien, Paul; Baker, Daniel N.; Ogasawara, Keiichi; Fennell, Joseph; Christian, Eric; Claudepierre, Seth; Livi, Stefano; Desai, Mihir; Li, Xinlin; Jaynes, Allison; Turner, Drew; Jones, Ashley; Schiller, Quintin

    2016-07-01

    We describe recent observations of the Earth's radiation belts made by instruments on board the Van Allen Probes mission, particularly the Relativistic Electron Proton Telescope (REPT) and the Magnetic Electron Ion spectrometer (MagEIS). These observations have significantly advanced our understanding of terrestrial radiation belt dynamics. The Van Allen Probes mission comprises two identically instrumented spacecraft which were launched 31 August, 2012 into low-inclination lapping equatorial orbits. The orbit periods are about 9 hours, with perigees and apogees of of ~600 km and 5.8 RE respectively. We discuss the new scientific findings of the Van Allen Probes mission regarding the physics of energization and loss of relativistic electrons and their implications for future low-cost missions, especially CubeSats. We describe the CeREs (a Compact Radiation belt Explorer) CubeSat mission currently being built at the Goddard Space Flight Center, and carrying on board, an innovative instrument, the Miniaturized Electron Proton Telescope (MERiT). The MERiT is a compact low-mass low-power instrument measuring electrons from a few keV to tens of MeV in multiple differential channels. MERiT is optimized to measure electron microbursts with a high time resolution of a few milliseconds. We present and discuss possible future scientific contributions from CeREs.

  10. Unravelling the Complexities of the Earth's Radiation Belts: Findings from the Van Allen Probes mission

    NASA Astrophysics Data System (ADS)

    Mauk, Barry; Fox, Nicola; Kessel, Ramona; Sibeck, David; Kanekal, Shri

    2014-05-01

    Within the first year of Van Allen Probe operations, team members made a series of highly publicized decisive discoveries concerning the structure and evolution of the Earth's radiation belts, the processes that energize particles there, and the locations where they operate. Nevertheless, much more extensive and less publicized findings from the Van Allen Probes suggest that Earth's radiation belts regions remain a highly complex and puzzling place. Although the relation between magnetic storm and radiation belt enhancements and loss has been emphasized, dynamics during non-storm periods has occasionally been shown to be dramatic. While emphasis has been placed on new findings regarding local non-adiabatic energization mechanisms, adiabatic mechanisms have also been shown to be important. Furthermore, the interplay between, and relative importance of, these and other energization processes remain uncertain. The role of seed populations has been highlighted, with some studies pointing to localized mechanisms and others pointing to the role of substorms in transporting and injecting such populations. Here we review some of the less publicized findings and future objectives of the Van Allen Probes mission to get a broader and in-depth view of present understanding of Earth's inner magnetosphere.

  11. A neural network approach for identifying particle pitch angle distributions in Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Souza, V. M.; Vieira, L. E. A.; Medeiros, C.; Da Silva, L. A.; Alves, L. R.; Koga, D.; Sibeck, D. G.; Walsh, B. M.; Kanekal, S. G.; Jauer, P. R.; Rockenbach, M.; Dal Lago, A.; Silveira, M. V. D.; Marchezi, J. P.; Mendes, O.; Gonzalez, W. D.; Baker, D. N.

    2016-04-01

    Analysis of particle pitch angle distributions (PADs) has been used as a means to comprehend a multitude of different physical mechanisms that lead to flux variations in the Van Allen belts and also to particle precipitation into the upper atmosphere. In this work we developed a neural network-based data clustering methodology that automatically identifies distinct PAD types in an unsupervised way using particle flux data. One can promptly identify and locate three well-known PAD types in both time and radial distance, namely, 90° peaked, butterfly, and flattop distributions. In order to illustrate the applicability of our methodology, we used relativistic electron flux data from the whole month of November 2014, acquired from the Relativistic Electron-Proton Telescope instrument on board the Van Allen Probes, but it is emphasized that our approach can also be used with multiplatform spacecraft data. Our PAD classification results are in reasonably good agreement with those obtained by standard statistical fitting algorithms. The proposed methodology has a potential use for Van Allen belt's monitoring.

  12. Gradual Diffusion and Punctuated Phase Space Density Enhancements of Highly Relativistic Electrons: Van Allen Probes Observations

    NASA Technical Reports Server (NTRS)

    Baker, D. N.; Jaynes, A. N.; Li, X.; Henderson, M. G.; Kanekal, S. G.; Reeves, G. D.; Spence, H. E.; Claudepierre, S. G.; Fennell, J. F.; Hudson, M. K.

    2014-01-01

    The dual-spacecraft Van Allen Probes mission has provided a new window into mega electron volt (MeV) particle dynamics in the Earth's radiation belts. Observations (up to E (is) approximately 10MeV) show clearly the behavior of the outer electron radiation belt at different timescales: months-long periods of gradual inward radial diffusive transport and weak loss being punctuated by dramatic flux changes driven by strong solar wind transient events. We present analysis of multi-MeV electron flux and phase space density (PSD) changes during March 2013 in the context of the first year of Van Allen Probes operation. This March period demonstrates the classic signatures both of inward radial diffusive energization and abrupt localized acceleration deep within the outer Van Allen zone (L (is) approximately 4.0 +/- 0.5). This reveals graphically that both 'competing' mechanisms of multi-MeV electron energization are at play in the radiation belts, often acting almost concurrently or at least in rapid succession.

  13. Spacecraft surface charging within geosynchronous orbit observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Sarno-Smith, Lois K.; Larsen, Brian A.; Skoug, Ruth M.; Liemohn, Michael W.; Breneman, Aaron; Wygant, John R.; Thomsen, Michelle F.

    2016-02-01

    Using the Helium Oxygen Proton Electron (HOPE) and Electric Field and Waves (EFW) instruments from the Van Allen Probes, we explored the relationship between electron energy fluxes in the eV and keV ranges and spacecraft surface charging. We present statistical results on spacecraft charging within geosynchronous orbit by L and MLT. An algorithm to extract the H+ charging line in the HOPE instrument data was developed to better explore intense charging events. Also, this study explored how spacecraft potential relates to electron number density, electron pressure, electron temperature, thermal electron current, and low-energy ion density between 1 and 210 eV. It is demonstrated that it is imperative to use both EFW potential measurements and the HOPE instrument ion charging line for examining times of extreme spacecraft charging of the Van Allen Probes. The results of this study show that elevated electron energy fluxes and high-electron pressures are present during times of spacecraft charging but these same conditions may also occur during noncharging times. We also show noneclipse significant negative charging events on the Van Allen Probes.

  14. Self-correcting multi-atlas segmentation

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Wilford, Andrew; Guo, Liang

    2016-03-01

    In multi-atlas segmentation, one typically registers several atlases to the new image, and their respective segmented label images are transformed and fused to form the final segmentation. After each registration, the quality of the registration is reflected by the single global value: the final registration cost. Ideally, if the quality of the registration can be evaluated at each point, independent of the registration process, which also provides a direction in which the deformation can further be improved, the overall segmentation performance can be improved. We propose such a self-correcting multi-atlas segmentation method. The method is applied on hippocampus segmentation from brain images and statistically significantly improvement is observed.

  15. [A study on Horace N. Allen's medicine and recognition of Korean body].

    PubMed

    Lee, Young Ah

    2011-12-31

    Je Jung Won was the first modern-style Government hospital built by the Korean King Ko-Jong in April 1885, and it was the medical missionary Horace Newton Allen(1858~1932) who made one of the greatest contributions to the establishment of the hospital. Allen was an American missionary. He graduated from Ohio Wesleyan University with a degree in theology in 1881, and completed one-yearcourse at Miami Medical College. In Korea and America he worked as a physician, a missionary, an American diplomatic minister to Korea and a Korean minister's secretary to America. While acting as a mediator between Korea and America, he knew and recorded the domestic and foreign situation of Korea during Gaehwagi(the civilized and enlightened age). Thus to study him is to understand Korea's Gaehwagi as well as to research American medical missionaries. During his stay in Korea(1884~1905), Allen steadily wrote diaries and letters about Korean politics, diplomacy, society, culture, and medicine. Thus his public/private record through diaries and letters(the quantity of these materials amounts to several thousands) supplements the Korean early modern era's historical record. However, until now these materials have received little scholarly attention from researchers except for a few historians of missionary work between Korea and America, or of Korean modern medicine. I intended to use these materials to suggest a new perspective on the study of Korean Gaehwagi. Allen, along with John W. Heron, who came to Seoul on June 21st 1885, treated about 10,460 Korean patients in the first year of the opening of JeJungWon. They made "the first annual report of the Korean Government Hospital". This report explained how Allen and Heron regarded and treated Korean patients. Allen's diaries, letters and other writings offer a realistic view of how the western people actually recognized the Korean people at that time. As a western doctor, Allen had an ambivalent attitude toward Korean medical concepts

  16. Constructing an un-biased whole body atlas from clinical imaging data by fragment bundling.

    PubMed

    Dorfer, Matthias; Donner, René; Langs, Georg

    2013-01-01

    Atlases have a tremendous impact on the study of anatomy and function, such as in neuroimaging, or cardiac analysis. They provide a means to compare corresponding measurements across populations, or model the variability in a population. Current approaches to construct atlases rely on examples that show the same anatomical structure (e.g., the brain). If we study large heterogeneous clinical populations to capture subtle characteristics of diseases, we cannot assume consistent image acquisition any more. Instead we have to build atlases from imaging data that show only parts of the overall anatomical structure. In this paper we propose a method for the automatic contruction of an un-biased whole body atlas from so-called fragments. Experimental results indicate that the fragment based atlas improves the representation accuracy of the atlas over an initial whole body template initialization.

  17. Brain Vascular Imaging Techniques

    PubMed Central

    Laviña, Bàrbara

    2016-01-01

    Recent major improvements in a number of imaging techniques now allow for the study of the brain in ways that could not be considered previously. Researchers today have well-developed tools to specifically examine the dynamic nature of the blood vessels in the brain during development and adulthood; as well as to observe the vascular responses in disease situations in vivo. This review offers a concise summary and brief historical reference of different imaging techniques and how these tools can be applied to study the brain vasculature and the blood-brain barrier integrity in both healthy and disease states. Moreover, it offers an overview on available transgenic animal models to study vascular biology and a description of useful online brain atlases. PMID:28042833

  18. [Atlas fractures].

    PubMed

    Schären, S; Jeanneret, B

    1999-05-01

    Fractures of the atlas account for 1-2% of all vertebral fractures. We divide atlas fractures into 5 groups: isolated fractures of the anterior arch of the atlas, isolated fractures of the posterior arch, combined fractures of the anterior and posterior arch (so-called Jefferson fractures), isolated fractures of the lateral mass and fractures of the transverse process. Isolated fractures of the anterior or posterior arch are benign and are treated conservatively with a soft collar until the neck pain has disappeared. Jefferson fractures are divided into stable and unstable fracture depending on the integrity of the transverse ligament. Stable Jefferson fractures are treated conservatively with good outcome while unstable Jefferson fractures are probably best treated operatively with a posterior atlanto-axial or occipito-axial stabilization and fusion. The authors preferred treatment modality is the immediate open reduction of the dislocated lateral masses combined with a stabilization in the reduced position using a transarticular screw fixation C1/C2 according to Magerl. This has the advantage of saving the atlanto-occipital joints and offering an immediate stability which makes immobilization in an halo or Minerva cast superfluous. In late instabilities C1/2 with incongruency of the lateral masses occurring after primary conservative treatment, an occipito-cervical fusion is indicated. Isolated fractures of the lateral masses are very rare and may, if the lateral mass is totally destroyed, be a reason for an occipito-cervical fusion. Fractures of the transverse processes may be the cause for a thrombosis of the vertebral artery. No treatment is necessary for the fracture itself.

  19. Computational analysis of LDDMM for brain mapping.

    PubMed

    Ceritoglu, Can; Tang, Xiaoying; Chow, Margaret; Hadjiabadi, Darian; Shah, Damish; Brown, Timothy; Burhanullah, Muhammad H; Trinh, Huong; Hsu, John T; Ament, Katarina A; Crocetti, Deana; Mori, Susumu; Mostofsky, Stewart H; Yantis, Steven; Miller, Michael I; Ratnanather, J Tilak

    2013-01-01

    One goal of computational anatomy (CA) is to develop tools to accurately segment brain structures in healthy and diseased subjects. In this paper, we examine the performance and complexity of such segmentation in the framework of the large deformation diffeomorphic metric mapping (LDDMM) registration method with reference to atlases and parameters. First we report the application of a multi-atlas segmentation approach to define basal ganglia structures in healthy and diseased kids' brains. The segmentation accuracy of the multi-atlas approach is compared with the single atlas LDDMM implementation and two state-of-the-art segmentation algorithms-Freesurfer and FSL-by computing the overlap errors between automatic and manual segmentations of the six basal ganglia nuclei in healthy subjects as well as subjects with diseases including ADHD and Autism. The high accuracy of multi-atlas segmentation is obtained at the cost of increasing the computational complexity because of the calculations necessary between the atlases and a subject. Second, we examine the effect of parameters on total LDDMM computation time and segmentation accuracy for basal ganglia structures. Single atlas LDDMM method is used to automatically segment the structures in a population of 16 subjects using different sets of parameters. The results show that a cascade approach and using fewer time steps can reduce computational complexity as much as five times while maintaining reliable segmentations.

  20. Mapping and Analysis of the Connectome of Sympathetic Premotor Neurons in the Rostral Ventrolateral Medulla of the Rat Using a Volumetric Brain Atlas

    PubMed Central

    Dempsey, Bowen; Le, Sheng; Turner, Anita; Bokiniec, Phil; Ramadas, Radhika; Bjaalie, Jan G.; Menuet, Clement; Neve, Rachael; Allen, Andrew M.; Goodchild, Ann K.; McMullan, Simon

    2017-01-01

    Spinally projecting neurons in the rostral ventrolateral medulla (RVLM) play a critical role in the generation of vasomotor sympathetic tone and are thought to receive convergent input from neurons at every level of the neuraxis; the factors that determine their ongoing activity remain unresolved. In this study we use a genetically restricted viral tracing strategy to definitively map their spatially diffuse connectome. We infected bulbospinal RVLM neurons with a recombinant rabies variant that drives reporter expression in monosynaptically connected input neurons and mapped their distribution using an MRI-based volumetric atlas and a novel image alignment and visualization tool that efficiently translates the positions of neurons captured in conventional photomicrographs to Cartesian coordinates. We identified prominent inputs from well-established neurohumoral and viscero-sympathetic sensory actuators, medullary autonomic and respiratory subnuclei, and supramedullary autonomic nuclei. The majority of inputs lay within the brainstem (88–94%), and included putative respiratory neurons in the pre-Bötzinger Complex and post-inspiratory complex that are therefore likely to underlie respiratory-sympathetic coupling. We also discovered a substantial and previously unrecognized input from the region immediately ventral to nucleus prepositus hypoglossi. In contrast, RVLM sympathetic premotor neurons were only sparsely innervated by suprapontine structures including the paraventricular nucleus, lateral hypothalamus, periaqueductal gray, and superior colliculus, and we found almost no evidence of direct inputs from the cortex or amygdala. Our approach can be used to quantify, standardize and share complete neuroanatomical datasets, and therefore provides researchers with a platform for presentation, analysis and independent reanalysis of connectomic data. PMID:28298886

  1. Mapping and Analysis of the Connectome of Sympathetic Premotor Neurons in the Rostral Ventrolateral Medulla of the Rat Using a Volumetric Brain Atlas.

    PubMed

    Dempsey, Bowen; Le, Sheng; Turner, Anita; Bokiniec, Phil; Ramadas, Radhika; Bjaalie, Jan G; Menuet, Clement; Neve, Rachael; Allen, Andrew M; Goodchild, Ann K; McMullan, Simon

    2017-01-01

    Spinally projecting neurons in the rostral ventrolateral medulla (RVLM) play a critical role in the generation of vasomotor sympathetic tone and are thought to receive convergent input from neurons at every level of the neuraxis; the factors that determine their ongoing activity remain unresolved. In this study we use a genetically restricted viral tracing strategy to definitively map their spatially diffuse connectome. We infected bulbospinal RVLM neurons with a recombinant rabies variant that drives reporter expression in monosynaptically connected input neurons and mapped their distribution using an MRI-based volumetric atlas and a novel image alignment and visualization tool that efficiently translates the positions of neurons captured in conventional photomicrographs to Cartesian coordinates. We identified prominent inputs from well-established neurohumoral and viscero-sympathetic sensory actuators, medullary autonomic and respiratory subnuclei, and supramedullary autonomic nuclei. The majority of inputs lay within the brainstem (88-94%), and included putative respiratory neurons in the pre-Bötzinger Complex and post-inspiratory complex that are therefore likely to underlie respiratory-sympathetic coupling. We also discovered a substantial and previously unrecognized input from the region immediately ventral to nucleus prepositus hypoglossi. In contrast, RVLM sympathetic premotor neurons were only sparsely innervated by suprapontine structures including the paraventricular nucleus, lateral hypothalamus, periaqueductal gray, and superior colliculus, and we found almost no evidence of direct inputs from the cortex or amygdala. Our approach can be used to quantify, standardize and share complete neuroanatomical datasets, and therefore provides researchers with a platform for presentation, analysis and independent reanalysis of connectomic data.

  2. Intraoperative virtual brain counseling

    NASA Astrophysics Data System (ADS)

    Jiang, Zhaowei; Grosky, William I.; Zamorano, Lucia J.; Muzik, Otto; Diaz, Fernando

    1997-06-01

    Our objective is to offer online real-tim e intelligent guidance to the neurosurgeon. Different from traditional image-guidance technologies that offer intra-operative visualization of medical images or atlas images, virtual brain counseling goes one step further. It can distinguish related brain structures and provide information about them intra-operatively. Virtual brain counseling is the foundation for surgical planing optimization and on-line surgical reference. It can provide a warning system that alerts the neurosurgeon if the chosen trajectory will pass through eloquent brain areas. In order to fulfill this objective, tracking techniques are involved for intra- operativity. Most importantly, a 3D virtual brian environment, different from traditional 3D digitized atlases, is an object-oriented model of the brain that stores information about different brain structures together with their elated information. An object-oriented hierarchical hyper-voxel space (HHVS) is introduced to integrate anatomical and functional structures. Spatial queries based on position of interest, line segment of interest, and volume of interest are introduced in this paper. The virtual brain environment is integrated with existing surgical pre-planning and intra-operative tracking systems to provide information for planning optimization and on-line surgical guidance. The neurosurgeon is alerted automatically if the planned treatment affects any critical structures. Architectures such as HHVS and algorithms, such as spatial querying, normalizing, and warping are presented in the paper. A prototype has shown that the virtual brain is intuitive in its hierarchical 3D appearance. It also showed that HHVS, as the key structure for virtual brain counseling, efficiently integrates multi-scale brain structures based on their spatial relationships.This is a promising development for optimization of treatment plans and online surgical intelligent guidance.

  3. Probabilistic atlas and geometric variability estimation to drive tissue segmentation.

    PubMed

    Xu, Hao; Thirion, Bertrand; Allassonnière, Stéphanie

    2014-09-10

    Computerized anatomical atlases play an important role in medical image analysis. While an atlas usually refers to a standard or mean image also called template, which presumably represents well a given population, it is not enough to characterize the observed population in detail. A template image should be learned jointly with the geometric variability of the shapes represented in the observations. These two quantities will in the sequel form the atlas of the corresponding population. The geometric variability is modeled as deformations of the template image so that it fits the observations. In this paper, we provide a detailed analysis of a new generative statistical model based on dense deformable templates that represents several tissue types observed in medical images. Our atlas contains both an estimation of probability maps of each tissue (called class) and the deformation metric. We use a stochastic algorithm for the estimation of the probabilistic atlas given a dataset. This atlas is then used for atlas-based segmentation method to segment the new images. Experiments are shown on brain T1 MRI datasets.

  4. Multiscale modeling for image analysis of brain tumor studies.

    PubMed

    Bauer, Stefan; May, Christian; Dionysiou, Dimitra; Stamatakos, Georgios; Büchler, Philippe; Reyes, Mauricio

    2012-01-01

    Image-based modeling of tumor growth combines methods from cancer simulation and medical imaging. In this context, we present a novel approach to adapt a healthy brain atlas to MR images of tumor patients. In order to establish correspondence between a healthy atlas and a pathologic patient image, tumor growth modeling in combination with registration algorithms is employed. In a first step, the tumor is grown in the atlas based on a new multiscale, multiphysics model including growth simulation from the cellular level up to the biomechanical level, accounting for cell proliferation and tissue deformations. Large-scale deformations are handled with an Eulerian approach for finite element computations, which can operate directly on the image voxel mesh. Subsequently, dense correspondence between the modified atlas and patient image is established using nonrigid registration. The method offers opportunities in atlas-based segmentation of tumor-bearing brain images as well as for improved patient-specific simulation and prognosis of tumor progression.

  5. Effect of the orbital debris environment on the high-energy Van Allen proton belt

    NASA Technical Reports Server (NTRS)

    Konradi, Andrei

    1988-01-01

    The lifetimes of high-energy (greater than 55 MeV) protons in the Van Allen radiation belt are calculated, assuming that in time the protons will collide with and be absorbed by particulate orbiting material. The calculations are based on the NASA/DoD Civil Needs Database for orbital debris (Gaines, 1966) and moderate assumptions of future space traffic. It is found that the lifetimes of high-energy protons below 1500 km will decrease, leading to a noticeable redution in their fluxes.

  6. Cognition About the Creative Process – Interview With Dr Andrew P. Allen

    PubMed Central

    Allen, Andrew P.; Loughnane, Lynda

    2016-01-01

    What is the relationship between the creative process and cognition and perception? Lynda Loughnane, a master’s student in Art and Process in Crawford College of Art and Design, Cork, Ireland interviewed Dr Andrew P. Allen about the subject. Areas covered include mindfulness, Type 1 and Type 2 thinking, stage theories of creativity, engagement with the art process and the artwork, phenomenology and consciousness with and without self report. The interview was constructed to cover a wide range of subject matter, so as to gather as much information as possible in layman's language about the cognitive process in relation to creativity and interaction with art. PMID:27872674

  7. Evaluation of Single Board Computers for the Antenna Controller at the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Harp, Gerald R.

    2002-12-01

    We review a variety off-the-shelf single board computers being considered for application in the Allen Telescope Array (ATA) for antenna control. The evaluation process used the following procedure: we developed an equivalent small program on each computer. This program communicates over a local area network (Ethernet) to a remote host, and makes some simple tests of the network bandwidth. The controllers are evaluated according to 1) the measured performance and 2) the time it takes to develop the software. Based on these tests we rate each controller and choose one based on the Ajile aJ-100 processor for application at the ATA.

  8. Science Highlights from the RBSP-ECT Particle Instrument Suite on NASA's Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Spence, Harlan

    2014-05-01

    The NASA Van Allen Probes mission includes an instrument suite known as the Radiation Belt Storm Probes (RBSP) - Energetic Particle, Composition, and Thermal Plasma (ECT) suite. RBSP-ECT contains a well-proven complement of particle instruments to ensure the highest quality measurements ever made in the radiation belts and the inner magnetosphere. The coordinated RBSP-ECT particle measurements, analyzed in combination with fields and waves observations and state of-the-art theory and modeling, provide new understanding on the acceleration, global distribution, and variability of radiation belt electrons and ions, key science objectives of NASA's Living With a Star program and the Van Allen Probes mission. The RBSP-ECT suite consists of three highly-coordinated instruments: the Helium Oxygen Proton Electron (HOPE) spectrometer, the Magnetic Electron Ion Spectrometer (MagEIS), and the Relativistic Electron Proton Telescope (REPT). Collectively these three instrument types cover comprehensively the full electron and ion spectra from one eV to 10's of MeV with sufficient energy resolution, pitch angle coverage and resolution, and with composition measurements in the critical energy range up to 50 keV and also from a few to 50 MeV/nucleon. All three instruments are based on measurement techniques proven in the radiation belts, then optimized to provide unambiguous separation of ions and electrons and clean energy responses even in the presence of extreme penetrating background environments. In this presentation, we summarize overall ECT science goals and then show scientific results derived from the ECT suite on the dual Van Allen Probes spacecraft to date. Mission operations began only in late October 2012, and we have now achieved significant results. Results presented here will include substantial progress toward resolving primary Van Allen Probes science targets, such as: the relative role of localized acceleration versus transport-generated particle acceleration

  9. Evaluation of effects of groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant, Shelby County, Tennessee

    USGS Publications Warehouse

    Haugh, Connor J.

    2016-08-10

    The Mississippi Embayment Regional Aquifer Study groundwater-flow model was used to simulate the potential effects of future groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant in Shelby County, Tennessee. The scenario used in the simulation consisted of a 30-year average withdrawal period followed by a 30-day maximum withdrawal period. Effects of withdrawals at the Allen plant site on the Mississippi embayment aquifer system were evaluated by comparing the difference in simulated water levels in the aquifers at the end of the 30-year average withdrawal period and at the end of the scenario to a base case without the Allen combined-cycle combustion turbine plant withdrawals. Simulated potentiometric surface declines in the Memphis aquifer at the Allen plant site were about 7 feet at the end of the 30-year average withdrawal period and 11 feet at the end of the scenario. The affected area of the Memphis aquifer at the Allen plant site as delineated by the 4-foot potentiometric surface-decline contour was 2,590 acres at the end of the 30-year average withdrawal period and 11,380 acres at the end of the scenario. Simulated declines in the underlying Fort Pillow aquifer and overlying shallow aquifer were both less than 1 foot at the end of the 30-year average withdrawal period and the end of the scenario.

  10. Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template.

    PubMed

    Majka, Piotr; Chaplin, Tristan A; Yu, Hsin-Hao; Tolpygo, Alexander; Mitra, Partha P; Wójcik, Daniel K; Rosa, Marcello G P

    2016-08-01

    The marmoset is an emerging animal model for large-scale attempts to understand primate brain connectivity, but achieving this aim requires the development and validation of procedures for normalization and integration of results from many neuroanatomical experiments. Here we describe a computational pipeline for coregistration of retrograde tracing data on connections of cortical areas into a 3D marmoset brain template, generated from Nissl-stained sections. The procedure results in a series of spatial transformations that are applied to the coordinates of labeled neurons in the different cases, bringing them into common stereotaxic space. We applied this procedure to 17 injections, placed in the frontal lobe of nine marmosets as part of earlier studies. Visualizations of cortical patterns of connections revealed by these injections are supplied as Supplementary Materials. Comparison between the results of the automated and human-based processing of these cases reveals that the centers of injection sites can be reconstructed, on average, to within 0.6 mm of coordinates estimated by an experienced neuroanatomist. Moreover, cell counts obtained in different areas by the automated approach are highly correlated (r = 0.83) with those obtained by an expert, who examined in detail histological sections for each individual. The present procedure enables comparison and visualization of large datasets, which in turn opens the way for integration and analysis of results from many animals. Its versatility, including applicability to archival materials, may reduce the number of additional experiments required to produce the first detailed cortical connectome of a primate brain. J. Comp. Neurol. 524:2161-2181, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  11. Construction and Evaluation of Quantitative Small-Animal PET Probabilistic Atlases for [18F]FDG and [18F]FECT Functional Mapping of the Mouse Brain

    PubMed Central

    Casteels, Cindy; Vunckx, Kathleen; Aelvoet, Sarah-Ann; Baekelandt, Veerle; Bormans, Guy; Van Laere, Koen; Koole, Michel

    2013-01-01

    Automated voxel-based or pre-defined volume-of-interest (VOI) analysis of small-animal PET data in mice is necessary for optimal information usage as the number of available resolution elements is limited. We have mapped metabolic ([18F]FDG) and dopamine transporter ([18F]FECT) small-animal PET data onto a 3D Magnetic Resonance Microscopy (MRM) mouse brain template and aligned them in space to the Paxinos co-ordinate system. In this way, ligand-specific templates for sensitive analysis and accurate anatomical localization were created. Next, using a pre-defined VOI approach, test-retest and intersubject variability of various quantification methods were evaluated. Also, the feasibility of mouse brain statistical parametric mapping (SPM) was explored for [18F]FDG and [18F]FECT imaging of 6-hydroxydopamine-lesioned (6-OHDA) mice. Methods Twenty-three adult C57BL6 mice were scanned with [18F]FDG and [18F]FECT. Registrations and affine spatial normalizations were performed using SPM8. [18F]FDG data were quantified using (1) an image-derived-input function obtained from the liver (cMRglc), using (2) standardized uptake values (SUVglc) corrected for blood glucose levels and by (3) normalizing counts to the whole-brain uptake. Parametric [18F]FECT binding images were constructed by reference to the cerebellum. Registration accuracy was determined using random simulated misalignments and vectorial mismatch determination. Results Registration accuracy was between 0.21–1.11 mm. Regional intersubject variabilities of cMRglc ranged from 15.4% to 19.2%, while test-retest values were between 5.0% and 13.0%. For [18F]FECT uptake in the caudate-putamen, these values were 13.0% and 10.3%, respectively. Regional values of cMRglc positively correlated to SUVglc measured within the 45–60 min time frame (spearman r = 0.71). Next, SPM analysis of 6-OHDA-lesioned mice showed hypometabolism in the bilateral caudate-putamen and cerebellum, and an unilateral striatal decrease in DAT

  12. Inner Magnetosphere keV Ion Drift Path Boundaries as Observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Strangeway, R. J.; Zhang, J.; Larsen, B.

    2014-12-01

    The drifts of keV ions in the inner magnetosphere are controlled by both electric field drifts and gradient and curvature (i.e., magnetic field) drifts, and further the magnetic field drifts oppose the corotation electric field drift in the dusk local time sector. Consequently, the ion drift paths can be quite complicated with the medium-energy ions drifting close to the Earth, but still being on open drift paths. In addition, structure in the energy-time spectrograms can be a consequence of either particle injection or particle loss. In order to distinguish between the two we will compare the energy-time spectrograms acquired with the Helium Oxygen Proton Electron (HOPE) mass spectrometer on board the Van Allen Probes with predictions of drift path boundaries. The simplest model assumes a uniform convection electric field and dipole model field, and we will use this a starting point for the comparison. The model can be modified to include shielding of the convection electric field, and rotation in local time of the zero-energy dusk-side stagnation point. As an additional check of the model we will compare the electric field used in the model with the electric field as measured by the Van Allen Probes, as well as the validity of using a dipole magnetic field through comparison with the measured magnetic field.

  13. Ion Spectral Structures Observed by the Van Allen Probes and Cluster

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

    2014-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

  14. An impenetrable barrier to ultrarelativistic electrons in the Van Allen radiation belts.

    PubMed

    Baker, D N; Jaynes, A N; Hoxie, V C; Thorne, R M; Foster, J C; Li, X; Fennell, J F; Wygant, J R; Kanekal, S G; Erickson, P J; Kurth, W; Li, W; Ma, Q; Schiller, Q; Blum, L; Malaspina, D M; Gerrard, A; Lanzerotti, L J

    2014-11-27

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. There is a region of dense cold plasma around the Earth known as the plasmasphere, the outer boundary of which is called the plasmapause. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary, with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location. Recent observations have revealed unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than five megaelectronvolts). Here we analyse an extended data set that reveals an exceedingly sharp inner boundary for the ultrarelativistic electrons. Additional, concurrently measured data reveal that this barrier to inward electron radial transport does not arise because of a physical boundary within the Earth's intrinsic magnetic field, and that inward radial diffusion is unlikely to be inhibited by scattering by electromagnetic transmitter wave fields. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can combine to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate.

  15. Collier Cobb and Allen D. Hole: Geologic mentors to early soil scientists

    NASA Astrophysics Data System (ADS)

    Brevik, Eric C.

    Many influential individuals involved in the early US soil survey program were trained as geologists rather than as agronomists or soil scientists. Several geology departments served as pipelines for students interested in a career in soil survey. This paper looks at the professional history of two early mentors of these geologists turned soil surveyors and some of the students they sent on to the US soil survey and other soil science careers. Collier Cobb sent over 10 students to the soil survey starting in 1900 when US soil survey was in its infancy, including individuals of note such as Hugh H. Bennett, George N. Coffey, Williamson E. Hearn, and Thomas D. Rice. Allen D. Hole worked on soil surveys for the state of Indiana and sent over a dozen students on to US soil survey careers between 1911 and 1937, including Mark Baldwin and James Thorp. Francis Hole and Ralph McCracken, other students of Allen Hole, also went on to have distinguished soil science careers. These mentors and students clearly show the close ties that existed between soil science and geology in the United States during the early 1900s.

  16. Collier Cobb and Allen D. Hole: Geologic Mentors to Early American Soil Scientists

    NASA Astrophysics Data System (ADS)

    Brevik, E. C.

    2012-04-01

    Many influential individuals involved in the early United States soil survey program were trained as geologists rather than as agronomists or soil scientists. Several geology departments served as pipelines for students interested in a career in soil survey. This presentation looks at the professional history of two early mentors of these geologists turned soil surveyors and some of the students they sent on to the U.S. soil survey and other soil science careers. Collier Cobb (University of North Carolina) sent over 10 students to the soil survey starting in 1900 when U.S. soil survey was in its infancy, including individuals of note such as Hugh H. Bennett, George N. Coffey, Williamson E. Hearn, and Thomas D. Rice. Allen D. Hole (Earlham College, Indiana) worked on soil surveys for the state of Indiana and sent over a dozen students on to U.S. soil survey careers between 1911 and 1937, including Mark Baldwin and James Thorp. Francis Hole and Ralph McCracken, other students of Allen Hole, also went on to have distinguished soil science careers. These mentors and students clearly show the close ties that existed between soil science and geology in the United States during the early 1900s.

  17. Marine ecological-risk assessment pilot study for Allen Harbor, Narragansett Bay, Rhode Island. Professional paper

    SciTech Connect

    Johnston, R.K.; Munns, W.R.; Mueller, C.; Nelson, W.G.; Pesch, G.G.

    1992-01-01

    An ecological risk assessment framework was applied to characterize aquatic risks associated with hazardous waste disposal at Naval Construction Battalion Center (NCBC) Davisville, Rhode Island. An initial screening phase (I) assessed exposure and related that exposure to toxicological endpoints for bivalves, amphipods, sea urchins, and biomarker assays. Results showed little evidence of major contamination in sediments or tissues except for relatively high levels of polychlorinated biphenols (PBC), butyltins compounds (TBT), and fecal coliforms observed in Allen Harbor. Effects were detected in mussel physiology, sea urchin fertilization and development, biomarker responses, and soft shell clam histology. Possible sources of contamination and toxicity from the landfill leachate, surface runoff, and recreational boating were examined using a temporaland spatial sampling scheme. Chemical and toxicological information obtained implicated all three sources as affecting Allen Harbor water quality. Laboratory bioassays of landfill exposure media, employing a variety of marine species using acute and chronic endpoints, are being used to provide data for the development of an exposure-response model for risk to the marine environment. The model will define current risk and provide an interpretive framework for long-term monitoring.

  18. Coordinated Radio and High-Energy Observations of Cygnus X-3 with the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Williams, Peter K. G.; Bower, G. C.; Tomsick, J. A.; Allen Telescope Array Team

    2011-01-01

    The microquasar Cygnus X-3 is one of the few Galactic sources known to produce relativistic jets and can be one of the brightest radio sources in the Galaxy when flaring. In late 2009 it became the first such system to be seen in the gamma-ray regime with detections by both AGILE and Fermi. We have observed Cyg X-3 at 3 GHz every 5 days for the past six months with the Allen Telescope Array in conjunction with space-based X-ray (INTEGRAL, RXTE) and gamma-ray (Fermi) observations. We present results from both the long-term dataset and intensive observing sessions in which we obtain the radio lightcurve of Cyg X-3 on 10-minute timescales. We focus particularly on a May 2010 minor flare event for which we have coverage in all three bands.The first phase of the ATA was funded through generous grants from the Paul G. Allen Family Foundation. UC Berkeley, the SETI Institute, the National Science Foundation (Grant No. 0540599), Sun Microsystems, Xilinx, Nathan Myhrvold, Greg Papadopoulos, and other corporations and individual donors contributed additional funding.

  19. Void structure of O+ ions in the inner magnetosphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Nakayama, Y.; Ebihara, Y.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.; Kistler, L. M.; Tanaka, T.

    2016-12-01

    The Van Allen Probes Helium Oxygen Proton Electron instrument observed a new type of enhancement of O+ ions in the inner magnetosphere during substorms. As the satellite moved outward in the premidnight sector, the flux of the O+ ions with energy 10 keV appeared first in the energy-time spectrograms. Then, the enhancement of the flux spread toward high and low energies. The enhanced flux of the O+ ions with the highest energy remained, whereas the flux of the ions with lower energy vanished near apogee, forming what we call the void structure. The structure cannot be found in the H+ spectrogram. We studied the generation mechanism of this structure by using numerical simulation. We traced the trajectories of O+ ions in the electric and magnetic fields from the global magnetohydrodynamics simulation and calculated the flux of O+ ions in the inner magnetosphere in accordance with the Liouville theorem. The simulated spectrograms are well consistent with the ones observed by Van Allen Probes. We suggest the following processes. (1) When magnetic reconnection starts, an intensive equatorward and tailward plasma flow appears in the plasma lobe. (2) The flow transports plasma from the lobe to the plasma sheet where the radius of curvature of the magnetic field line is small. (3) The intensive dawn-dusk electric field transports the O+ ions earthward and accelerates them nonadiabatically to an energy threshold; (4) the void structure appears at energies below the threshold.

  20. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  1. Observations and Simulations of Whistler-mode Waves Detected by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Bengtson, M.; Rosborough, S.; Stein, R. L.; Streltsov, A. V.; Matheny, M. M.

    2015-12-01

    In March of 2014, Van Allen Probe A observed several packets of whistler-mode waves while passing through the apogee of an orbit on the dayside magnetosphere. These waves were localized in regions of strong density inhomogeneity. For one observed wave, the wave maximum occurred within the center of the channel formed by a density enhancement. The other two waves were observed on either side of strong density depletion. We first determine the wave characteristics using data from Van Allen Probe A. Then, we use the observations to specify parameters in an electron MHD simulation to model the propagation of whistler-mode waves inside density structures. These observations and simulations demonstrate how whistler-mode waves can become trapped inside density structures, a phenomenon known as ducting. The density ducts serve to guide the whistler-mode waves into the earth's radiation belt while minimizing damping effects. The purpose of this research is to understand the role of density ducts in guiding whistler-mode waves, which will have important applications for remediation of energetic particles from the radiation belt.

  2. Electric and magnetic radial diffusion coefficients using the Van Allen probes data

    NASA Astrophysics Data System (ADS)

    Ali, Ashar F.; Malaspina, David M.; Elkington, Scot R.; Jaynes, Allison N.; Chan, Anthony A.; Wygant, John; Kletzing, Craig A.

    2016-10-01

    ULF waves are a common occurrence in the inner magnetosphere and they contribute to particle motion, significantly, at times. We used the magnetic and the electric field data from the Electric and Magnetic Field Instrument Suite and Integrated Sciences (EMFISIS) and the Electric Field and Waves instruments (EFW) on board the Van Allen Probes to estimate the ULF wave power in the compressional component of the magnetic field and the azimuthal component of the electric field, respectively. Using L∗, Kp, and magnetic local time (MLT) as parameters, we conclude that the noon sector contains higher ULF Pc-5 wave power compared with the other MLT sectors. The dawn, dusk, and midnight sectors have no statistically significant difference between them. The drift-averaged power spectral densities are used to derive the magnetic and the electric component of the radial diffusion coefficient. Both components exhibit little to no energy dependence, resulting in simple analytic models for both components. More importantly, the electric component is larger than the magnetic component by one to two orders of magnitude for almost all L∗ and Kp; thus, the electric field perturbations are more effective in driving radial diffusion of charged particles in the inner magnetosphere. We also present a comparison of the Van Allen Probes radial diffusion coefficients, including the error estimates, with some of the previous published results. This allows us to gauge the large amount of uncertainty present in such estimates.

  3. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    PubMed Central

    Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

    2016-01-01

    The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

  4. Type II Isopentenyl Diphosphate Isomerase: Probing the Mechanism with Alkyne/Allene Diphosphate Substrate Analogues†

    PubMed Central

    Sharma, Nagendra K.; Pan, Jian-Jung; Poulter, C. Dale

    2010-01-01

    Isopentenyl diphosphate isomerase (IDI) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the basic five-carbon building blocks of isoprenoid molecules. Two structurally unrelated classes of IDI are known. Type I IPP isomerase (IDI-1) utilizes a divalent metal in a protonation-deprotonation reaction. In contrast, the type II enzyme (IDI-2) requires reduced flavin, raising the possibility that the reaction catalyzed by IDI-2 involves the net addition/abstraction of a hydrogen atom. As part of our studies of the mechanism of isomerization for IDI-2, we synthesized allene and alkyne substrate analogues for the enzyme. These molecules are predicted to be substantially less reactive toward proton addition than IPP and DMAPP, but have similar reactivities toward hydrogen atom addition. This prediction was verified by calculations of gas phase heats of reaction for addition of a proton and of a hydrogen atom to 1-butyne (3) and 1,2-butadiene (4) to form the 1-buten-2-yl carbocation and radical, respectively, and related affinities for 2-methyl-1-butene (5) and 2-methyl-2-butene (6) using G3MP2B3 and CBS-QB3 protocols. Alkyne 1-OPP and allene 2-OPP were not substrates for Thermus thermophilus IDI-2 or Escherichia coli IDI-1, but instead were competitive inhibitors. The experimental and computational results are consistent with a protonation-deprotonation mechanism for the enzyme-catalyzed isomerization of IPP and DMAPP. PMID:20560533

  5. Impacts of intense inward and outward ULF wave radial diffusion on the Van Allen belts

    NASA Astrophysics Data System (ADS)

    Mann, Ian; Ozeke, Louis; Rae, I. Jonathan; Murphy, Kyle

    2016-07-01

    During geomagnetic storms, the power in ultra-low frequency (ULF) waves can be orders of magnitude larger than that predicted by statistics determined from an entire solar cycle. This is especially true during the main phase and early recovery phase. These periods of enhanced storm-time ULF wave power can have significant impacts on the morphology and structure of the Van Allen belts. Either fast inward or outward radial diffusion can result, depending on the profiles of the electron phase space density and the outer boundary condition at the edge of the belts. Small changes in the time sequence of powerful ULF waves, and the time sequence of any magnetopause shadowing or the recovery of plamasheet sources relative to the ULF wave occurrence, have a remarkable impact on the resulting structure of the belts. The overall impact of the enhanced ULF wave power is profound, but the response can be very different depending on the available source flux in the plasmasheet. We review these impacts by examining ultra-relativistic electron dynamics during seemingly different storms during the Van Allen Probe era, including during the Baker et al. third radiation belt, and show the observed behaviour can be largely explained by differences in the time sequence of events described above.

  6. Observations of Quasi-Periodic Whistler Mode Waves by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Hospodarsky, George; Wilkinson, Darrelle; Kurth, William; Kletzing, Craig; Santolik, Ondrej

    2016-10-01

    Observed in Earth's inner magnetosphere, quasi-periodic whistler mode emissions (QP) are electromagnetic waves in the frequency range from a few hundred Hz to a few kHz that exhibit a periodic modulation (typically a few minutes) of their wave intensity. These waves were first detected at high latitude ground stations, but more recently have been observed by a number of spacecraft, including the twin Van Allen Probes. The Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) instrument simultaneously measures the vector wave magnetic field and electric field, allowing wave propagation parameters, such as wave normal angle and Poynting vector, to be obtained. Almost four years of Van Allen Probes data have been examined and a statistical survey of the occurrence and properties of the QP emissions has been performed. The QP emissions were found to have periods ranging from 1 to 16 minutes with events lasting from less than 1 hour up to 6 hours. Some events were detected on successive orbits and a number of events were simultaneously detected by both spacecraft, even during large spacecraft separations, providing an opportunity to investigate the source and propagation properties of these waves.

  7. Multi-atlas learner fusion: An efficient segmentation approach for large-scale data.

    PubMed

    Asman, Andrew J; Huo, Yuankai; Plassard, Andrew J; Landman, Bennett A

    2015-12-01

    We propose multi-atlas learner fusion (MLF), a framework for rapidly and accurately replicating the highly accurate, yet computationally expensive, multi-atlas segmentation framework based on fusing local learners. In the largest whole-brain multi-atlas study yet reported, multi-atlas segmentations are estimated for a training set of 3464 MR brain images. Using these multi-atlas estimates we (1) estimate a low-dimensional representation for selecting locally appropriate example images, and (2) build AdaBoost learners that map a weak initial segmentation to the multi-atlas segmentation result. Thus, to segment a new target image we project the image into the low-dimensional space, construct a weak initial segmentation, and fuse the trained, locally selected, learners. The MLF framework cuts the runtime on a modern computer from 36 h down to 3-8 min - a 270× speedup - by completely bypassing the need for deformable atlas-target registrations. Additionally, we (1) describe a technique for optimizing the weak initial segmentation and the AdaBoost learning parameters, (2) quantify the ability to replicate the multi-atlas result with mean accuracies approaching the multi-atlas intra-subject reproducibility on a testing set of 380 images, (3) demonstrate significant increases in the reproducibility of intra-subject segmentations when compared to a state-of-the-art multi-atlas framework on a separate reproducibility dataset, (4) show that under the MLF framework the large-scale data model significantly improve the segmentation over the small-scale model under the MLF framework, and (5) indicate that the MLF framework has comparable performance as state-of-the-art multi-atlas segmentation algorithms without using non-local information.

  8. From the IGY to the IHY: A Changing View of the Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Hudson, M. K.

    2006-12-01

    Discovery of the Van Allen radiation belts by instrumentation flown on Explorer 1 in 1958 was the first major discovery of the Space Age. A view of the belts as static inner and outer zones of energetic particles with different sources, a double-doughnut encircling the Earth, became iconic to the point that their dynamic behavior and solar connection receded from public awareness and apparent scientific import. Then the Cycle 23 maximum in solar activity arrived in 1989-1991, the first approaching the activity level of the International Geophysical Year of 1957-58, when the Van Allen belts were first discovered. Delay in launch of the NASA-Air Force Combined Radiation Release and Effects Satellite, following the Challenger accident in 1986, led to having the right instruments in the right orbit at the right time to detect prompt injection of outer belt electrons and solar energetic protons into the `slot region' between the inner and outer belts, forming new trapped populations which lasted for years in an otherwise benign location. This event in March 1991, along with the great geomagnetic storm of March 1989, and our increased dependence on space technology since the early Explorer days, led to a resurgence of interest in the Van Allen radiation belts and understanding of their connectivity to the Sun. Additional instrumentation from NASA's International Solar Terrestrial Physics Program, the Solar Anomalous and Magnetospheric Particle Explorer (SAMPEX) and IMAGE spacecraft from the Explorer program, NOAA and DOD spacecraft, and improved worldwide linkages of groundbased measurements have contributed much since 1991 to our understanding of the dynamic characteristics of the Van Allen belts. Further, the presence of continuous solar wind measurements beginning with the launch of WIND in 1994, and SOHO images of Coronal Mass Ejections and coronal hole sources of high speed solar wind flow have filled in the connection with solar activity qualitatively anticipated

  9. Cross-scale observations of the 2015 St. Patrick's day storm: THEMIS, Van Allen Probes, and TWINS

    NASA Astrophysics Data System (ADS)

    Goldstein, J.; Angelopoulos, V.; De Pascuale, S.; Funsten, H. O.; Kurth, W. S.; LLera, K.; McComas, D. J.; Perez, J. D.; Reeves, G. D.; Spence, H. E.; Thaller, S. A.; Valek, P. W.; Wygant, J. R.

    2017-01-01

    We present cross-scale magnetospheric observations of the 17 March 2015 (St. Patrick's Day) storm, by Time History of Events and Macroscale Interactions during Substorms (THEMIS), Van Allen Probes (Radiation Belt Storm Probes), and Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS), plus upstream ACE/Wind solar wind data. THEMIS crossed the bow shock or magnetopause 22 times and observed the magnetospheric compression that initiated the storm. Empirical models reproduce these boundary locations within 0.7 RE. Van Allen Probes crossed the plasmapause 13 times; test particle simulations reproduce these encounters within 0.5 RE. Before the storm, Van Allen Probes measured quiet double-nose proton spectra in the region of corotating cold plasma. About 15 min after a 0605 UT dayside southward turning, Van Allen Probes captured the onset of inner magnetospheric convection, as a density decrease at the moving corotation-convection boundary (CCB) and a steep increase in ring current (RC) proton flux. During the first several hours of the storm, Van Allen Probes measured highly dynamic ion signatures (numerous injections and multiple spectral peaks). Sustained convection after ˜1200 UT initiated a major buildup of the midnight-sector ring current (measured by RBSP A), with much weaker duskside fluxes (measured by RBSP B, THEMIS a and THEMIS d). A close conjunction of THEMIS d, RBSP A, and TWINS 1 at 1631 UT shows good three-way agreement in the shapes of two-peak spectra from the center of the partial RC. A midstorm injection, observed by Van Allen Probes and TWINS at 1740 UT, brought in fresh ions with lower average energies (leading to globally less energetic spectra in precipitating ions) but increased the total pressure. The cross-scale measurements of 17 March 2015 contain significant spatial, spectral, and temporal structure.

  10. Shape-based multifeature brain parcellation

    NASA Astrophysics Data System (ADS)

    Nadeem, Saad; Kaufman, Arie

    2016-03-01

    We present a novel approach to parcellate - delineate the anatomical feature (folds, gyri, sulci) boundaries - the brain cortex. Our approach is based on extracting the 3D brain cortical surface mesh from magnetic resonance (MR) images, computing the shape measures (area, mean curvature, geodesic, and travel depths) for this mesh, and delineating the anatomical feature boundaries using these measures. We use angle-area preserving mapping of the cortical surface mesh to a simpler topology (disk or rectangle) to aid in the visualization and delineation of these boundaries. Contrary to commonly used generic 2D brain image atlas-based approaches, we use 3D surface mesh data extracted from a given brain MR imaging data and its specific shape measures for the parcellation. Our method does not require any non-linear registration of a given brain dataset to a generic atlas and hence, does away with the structure similarity assumption critical to the atlas-based approaches. We evaluate our approach using Mindboggle manually labeled brain datasets and achieve the following accuracies: 72.4% for gyri, 78.5% for major sulci, and 98.4% for folds. These results warrant further investigation of this approach as an alternative or as an initialization to the atlas-based approaches.

  11. Direct estimation of patient attributes from anatomical MRI based on multi-atlas voting.

    PubMed

    Wu, Dan; Ceritoglu, Can; Miller, Michael I; Mori, Susumu

    MRI brain atlases are widely used for automated image segmentation, and in particular, recent developments in multi-atlas techniques have shown highly accurate segmentation results. In this study, we extended the role of the atlas library from mere anatomical reference to a comprehensive knowledge database with various patient attributes, such as demographic, functional, and diagnostic information. In addition to using the selected (heavily-weighted) atlases to achieve high segmentation accuracy, we tested whether the non-anatomical attributes of the selected atlases could be used to estimate patient attributes. This can be considered a context-based image retrieval (CBIR) approach, embedded in the multi-atlas framework. We first developed an image similarity measurement to weigh the atlases on a structure-by-structure basis, and then, the attributes of the multiple atlases were weighted to estimate the patient attributes. We tested this concept first by estimating age in a normal population; we then performed functional and diagnostic estimations in Alzheimer's disease patients. The accuracy of the estimated patient attributes was measured against the actual clinical data, and the performance was compared to conventional volumetric analysis. The proposed CBIR framework by multi-atlas voting would be the first step toward a knowledge-based support system for quantitative radiological image reading and diagnosis.

  12. On the generation of large amplitude spiky solitons by ultralow frequency earthquake emission in the Van Allen radiation belt

    SciTech Connect

    Mofiz, U. A.

    2006-08-15

    The parametric coupling between earthquake emitted circularly polarized electromagnetic radiation and ponderomotively driven ion-acoustic perturbations in the Van Allen radiation belt is considered. A cubic nonlinear Schroedinger equation for the modulated radiation envelope is derived, and then solved analytically. For ultralow frequency earthquake emissions large amplitude spiky supersonic bright solitons or subsonic dark solitons are found to be generated in the Van Allen radiation belt, detection of which can be a tool for the prediction of a massive earthquake may be followed later.

  13. Microgloma Sanders & Allen, 1973 (Nuculanidae) and Pristigloma Dall, 1900 (Pristiglomidae) (Pelecypoda) in the Campos Basin off Brazil

    PubMed Central

    Benaim, Natalia Pereira; Absalão, Ricardo Silva

    2011-01-01

    Abstract As a secondary result of oil prospecting in Brazil, samples from the Campos Basin continental slope became available. In these samples, specimens of the genera Microgloma Sanders & Allen, 1973 and Pristigloma Dall, 1900 were found. This contribution provides the southernmost record of the genus Microgloma, the first record of Microgloma mirmidina (Dautzenberg & Fischer 1897) from the western Atlantic, the descriptions of Microgloma macaron sp. n. and Microgloma nhanduti sp. n.as new species, and the shallowest record of Pristigloma alba Sanders & Allen 1973. PMID:22287903

  14. Parallel optimization of tumor model parameters for fast registration of brain tumor images

    NASA Astrophysics Data System (ADS)

    Zacharaki, Evangelia I.; Hogea, Cosmina S.; Shen, Dinggang; Biros, George; Davatzikos, Christos

    2008-03-01

    The motivation of this work is to register MR brain tumor images with a brain atlas. Such a registration method can make possible the pooling of data from different brain tumor patients into a common stereotaxic space, thereby enabling the construction of statistical brain tumor atlases. Moreover, it allows the mapping of neuroanatomical brain atlases into the patient's space, for segmenting brains and thus facilitating surgical or radiotherapy treatment planning. However, the methods developed for registration of normal brain images are not directly applicable to the registration of a normal atlas with a tumor-bearing image, due to substantial dissimilarity and lack of equivalent image content between the two images, as well as severe deformation or shift of anatomical structures around the tumor. Accordingly, a model that can simulate brain tissue death and deformation induced by the tumor is considered to facilitate the registration. Such tumor growth simulation models are usually initialized by placing a small seed in the normal atlas. The shape, size and location of the initial seed are critical for achieving topological equivalence between the atlas and patient's images. In this study, we focus on the automatic estimation of these parameters, pertaining to tumor simulation. In particular, we propose an objective function reflecting feature-based similarity and elastic stretching energy and optimize it with APPSPACK (Asynchronous Parallel Pattern Search), for achieving significant reduction of the computational cost. The results indicate that the registration accuracy is high in areas around the tumor, as well as in the healthy portion of the brain.

  15. Comparison of species-resolved energy spectra from ACE EPAM and Van Allen Probes RBSPICE

    NASA Astrophysics Data System (ADS)

    Patterson, J.; Manweiler, J. W.; Armstrong, T. P.; Lanzerotti, L. J.; Gerrard, A. J.; Gkioulidou, M.

    2013-12-01

    We present a comparison between energy spectra measured by the Advanced Composition Explorer (ACE) Electron Proton Alpha Monitor (EPAM) instrument and the Van Allen Probe Ion Composition Experiment (RBSPICE) for two significant and distinct events in early 2013. The first is an impulsive solar particle event on March 17th. While intense, this event presented no significant surprises in terms of its composition or anisotropy characteristics, thus providing a good baseline for response of the trapped radiation belts as observed by the Van Allen Probes. The second solar event occurred late May 22nd and early May 23rd. This event has a much greater concentration of medium and heavy ions than the St. Patrick's Day event, as well as having very peculiar energy spectra with evidence of two distinct populations. During the St. Patrick's Day Event, the energy spectra for helium, carbon, oxygen, neon, silicon, and iron all show the same spectral power law slope -3.1. The event shows strong anisotropy with intensities differing by a factor of four for both protons and Z>1 ions. The late May event also has strong anisotropy, and in the same directions as the St. Patrick's Day Event, but with very different composition and energy spectra. The spectra are much harder with power law spectral slopes of -0.5. Additionally, there is a significant spectral bump at 3 MeV/nuc for helium that is not present in the spectra of the heavier ions. The intensities of the heavier ions, however, show an increase that is an order of magnitude greater than the increase seen for helium. The March 17 RBSPICE observations show multiple injection events lasting for less than an hour each during the Van Allen Probes B apogees. These injections are seen in protons as well as Helium and only somewhat observed in Oxygen. Spectral slopes for the observations range from approximately -5 during quiet times to double peaked events with a spectral slope of approximately -2 at the beginning of the injection

  16. Generation and evaluation of an ultra-high-field atlas with applications in DBS planning

    NASA Astrophysics Data System (ADS)

    Wang, Brian T.; Poirier, Stefan; Guo, Ting; Parrent, Andrew G.; Peters, Terry M.; Khan, Ali R.

    2016-03-01

    Purpose Deep brain stimulation (DBS) is a common treatment for Parkinson's disease (PD) and involves the use of brain atlases or intrinsic landmarks to estimate the location of target deep brain structures, such as the subthalamic nucleus (STN) and the globus pallidus pars interna (GPi). However, these structures can be difficult to localize with conventional clinical magnetic resonance imaging (MRI), and thus targeting can be prone to error. Ultra-high-field imaging at 7T has the ability to clearly resolve these structures and thus atlases built with these data have the potential to improve targeting accuracy. Methods T1 and T2-weighted images of 12 healthy control subjects were acquired using a 7T MR scanner. These images were then used with groupwise registration to generate an unbiased average template with T1w and T2w contrast. Deep brain structures were manually labelled in each subject by two raters and rater reliability was assessed. We compared the use of this unbiased atlas with two other methods of atlas-based segmentation (single-template and multi-template) for subthalamic nucleus (STN) segmentation on 7T MRI data. We also applied this atlas to clinical DBS data acquired at 1.5T to evaluate its efficacy for DBS target localization as compared to using a standard atlas. Results The unbiased templates provide superb detail of subcortical structures. Through one-way ANOVA tests, the unbiased template is significantly (p <0.05) more accurate than a single-template in atlas-based segmentation and DBS target localization tasks. Conclusion The generated unbiased averaged templates provide better visualization of deep brain nuclei and an increase in accuracy over single-template and lower field strength atlases.

  17. Two-stage atlas subset selection in multi-atlas based image segmentation

    SciTech Connect

    Zhao, Tingting Ruan, Dan

    2015-06-15

    Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

  18. High-Throughput Analysis of Dynamic Gene Expression Associated with Sleep Deprivation and Recovery Sleep in the Mouse Brain

    DTIC Science & Technology

    2006-12-01

    Gene Expression Associated with Sleep Deprivation and Recovery Sleep in the Mouse Brain PRINCIPAL INVESTIGATOR: Ed Lein, Ph.D...CONTRACTING ORGANIZATION: Allen Institute for Brain Science Seattle, WA 98103 REPORT DATE...Recovery Sleep in the Mouse Brain 5b. GRANT NUMBER W81XWH-06-1-0131 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Ed Lein, Ph.D

  19. Expert-validated CSF segmentation of MNI atlas enhances accuracy of virtual glioma growth patterns.

    PubMed

    Amelot, A; Stretton, E; Delingette, H; Ayache, N; Froelich, S; Mandonnet, E

    2015-01-01

    Biomathematical modeling of glioma growth has been developed to optimize treatments delivery and to evaluate their efficacy. Simulations currently make use of anatomical knowledge from standard MRI atlases. For example, cerebrospinal fluid (CSF) spaces are obtained by automatic thresholding of the MNI atlas, leading to an approximate representation of real anatomy. To correct such inaccuracies, an expert-revised CSF segmentation map of the MNI atlas was built. Several virtual glioma growth patterns of different locations were generated, with and without using the expert-revised version of the MNI atlas. The adequacy between virtual and radiologically observed growth patterns was clearly higher when simulations were based on the expert-revised atlas. This work emphasizes the need for close collaboration between clinicians and researchers in the field of brain tumor modeling.

  20. Remarkable new results for high-energy protons and electrons in the inner Van Allen belt regions

    NASA Astrophysics Data System (ADS)

    Baker, Daniel N.

    2016-04-01

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location.. Recent Van Allen Probes observations have revealed an unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than several megaelectronvolts). The data show an exceedingly sharp inner boundary for the ultrarelativistic electrons right at L=2.8. Additional, concurrently measured data reveal that this barrier to inward electron radial transport is likely due to scattering by powerful human electromagnetic transmitter (VLF) wave fields. We show that weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere due to manmade signals can act to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate. Inside of this distance, the Van Allen Probes data show that high energy (20 -100 MeV) protons have a double belt structure with a stable peak of flux at L~1.5 and a much more variable belt peaking at L~2.3.

  1. Choctaw Leadership in Oklahoma: The Allen Wright Family and Education in the Nineteenth and Early Twentieth Centuries

    ERIC Educational Resources Information Center

    Noley, Grayson; Smith, Joan K.; Vaughn, Courtney; Cesar, Dana

    2009-01-01

    Against the backdrop of internal colonialism, this article examines the educational and social lives of Allen Wright and his children to better understand how this Choctaw family successfully navigated the pressures of dual cultures by: (1) providing the socio-political context of the indigenous culture prior to Wright's birth; (2) chronicling and…

  2. Rearrangement of vinyl allene oxide geometric isomers to cyclopentenones. Further computational insights with biologically relevant model systems.

    PubMed

    González-Pérez, Adán B; Grechkin, Alexander; de Lera, Ángel R

    2017-03-28

    Pathways for the rearrangement of the E and Z isomers of allyl- and methyl-substituted vinyl allene oxides to stereodefined cyclopentenones have been studied by DFT computations. Regardless of the reactant geometry, cis-configured cyclopentenones are found to be formed in a stepwise cascade comprising as key steps the ring opening of the oxirane to give an oxidopentadienyl diradical, its isomerization, and electrocyclization. An allyl substituent at the Csp(3) atom of the starting vinyl allene oxide induces opposite effects on the activation energies for ring opening: a decrease owing to assistance by homoconjugation for the out motion and an increase due to the stereoelectronic stabilization of the reactant. As a result, allyl- and methyl-substituted vinyl allene oxides exhibit comparable activation energies. Only model systems with crotyl substituents afford lower activation energies than the methyl counterparts due to the additional stabilization of the forming charge deficiency at a secondary carbon by homoconjugation. Moreover, upon homoconjugative interaction reactants of Z geometry are predicted to undergo cyclization more readily than the E isomers. The results with Z-crotyl substituent are congruent with the spontaneous rearrangement of natural vinyl allene oxide derived from α-linolenic acid to a racemic cis-cyclopentenone (12-oxo-PDA).

  3. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

    ScienceCinema

    Holberg, Leo; Mills, Allen [NIST

    2016-07-12

    Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  4. Rapid Asymmetric Synthesis of Disubstituted Allenes by Coupling of Flow‐Generated Diazo Compounds and Propargylated Amines

    PubMed Central

    Poh, Jian‐Siang; Makai, Szabolcs; von Keutz, Timo; Tran, Duc N.; Battilocchio, Claudio; Pasau, Patrick

    2017-01-01

    Abstract We report herein the asymmetric coupling of flow‐generated unstabilized diazo compounds and propargylated amine derivatives, using a new pyridinebis(imidazoline) ligand, a copper catalyst and base. The reaction proceeds rapidly, generating chiral allenes in 10–20 minutes with high enantioselectivity (89–98 % de/ee), moderate yields and a wide functional group tolerance. PMID:28075518

  5. A finite difference method for a conservative Allen-Cahn equation on non-flat surfaces

    NASA Astrophysics Data System (ADS)

    Kim, Junseok; Jeong, Darae; Yang, Seong-Deog; Choi, Yongho

    2017-04-01

    We present an efficient numerical scheme for the conservative Allen-Cahn (CAC) equation on various surfaces embedded in a narrow band domain in the three-dimensional space. We apply a quasi-Neumann boundary condition on the narrow band domain boundary using the closest point method. This boundary treatment allows us to use the standard Cartesian Laplacian operator instead of the Laplace-Beltrami operator. We apply a hybrid operator splitting method for solving the CAC equation. First, we use an explicit Euler method to solve the diffusion term. Second, we solve the nonlinear term by using a closed-form solution. Third, we apply a space-time-dependent Lagrange multiplier to conserve the total quantity. The overall scheme is explicit in time and does not need iterative steps; therefore, it is fast. A series of numerical experiments demonstrate the accuracy and efficiency of the proposed hybrid scheme.

  6. Long-duration exohiss waves outside the plasmasphere: observed by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhu, H.; Su, Z.; Xiao, F.; Zheng, H.; Wang, Y.; He, Z.; Shen, C.; Zhang, M.; Wang, S.; Kletzing, C.; Kurth, W. S.; Hospodarsky, G. B.; Spence, H. E.; Reeves, G. D.; Funsten, H. O.; Blake, J. B.; Baker, D. N.

    2014-12-01

    We report an exohiss event in the low-density trough region observed by Van Allen Probes on 2 February 2014. These exohiss waves are discovered in the wide MLT distribution [9.1,13.4] and low magnetic latitude, with narrow-band structure and weak intensity compared with plasmaspheric hiss. Using the Continue Waveform Burst Mode data and MAG data on the EMFISIS, we analyze the normal angle, electromagnetic planarity and anti~/parallel-propagating Poynting flux of exohiss wave. The results show indicate that exohiss waves are the result of plasmaspheric hiss leakage into the trough region. The dependence of the proportion of anti~/parallel-propagating Poynting flux on MLT can be explained by Landau damping associated with suprathermal eletrons.

  7. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    SciTech Connect

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-10-05

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth’s magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. In conclusion, simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. Finally, the current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  8. George Herbert Mead and the Allen controversy at the University of Wisconsin.

    PubMed

    Cook, Gary A

    2007-01-01

    This essay uses previously unpublished correspondence of George Herbert Mead to tell the story of his involvement in the aftermath of a political dispute that took place at the University of Wisconsin during the years 1914-1915. It seeks thereby to clarify the historical significance of an article he published on this controversy in late 1915. Taken together with relevant information about the educational activities of William H. Allen of the New York Bureau of Municipal Research, Mead's correspondence and article throw helpful light upon his understanding of how an educational survey of a university should proceed; they also show how he went about the task of evaluating a failed attempt at such a survey.

  9. Statistical distribution of EMIC wave spectra: Observations from Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, X.-J.; Li, W.; Thorne, R. M.; Angelopoulos, V.; Bortnik, J.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.

    2016-12-01

    It has been known that electromagnetic ion cyclotron (EMIC) waves can precipitate ultrarelativistic electrons through cyclotron resonant scattering. However, the overall effectiveness of this mechanism has yet to be quantified, because it is difficult to obtain the global distribution of EMIC waves that usually exhibit limited spatial presence. We construct a statistical distribution of EMIC wave frequency spectra and their intensities based on Van Allen Probes measurements from September 2012 to December 2015. Our results show that as the ratio of plasma frequency over electron gyrofrequency increases, EMIC wave power becomes progressively dominated by the helium band. There is a pronounced dawn-dusk asymmetry in the wave amplitude and the frequency spectrum. The frequency spectrum does not follow the commonly used single-peak Gaussian function. Incorporating these realistic EMIC wave frequency spectra into radiation belt models is expected to improve the quantification of EMIC wave scattering effects in ultrarelativistic electron dynamics.

  10. Van Allen Probes observations of oxygen cyclotron harmonic waves in the inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Usanova, M. E.; Malaspina, D. M.; Jaynes, A. N.; Bruder, R. J.; Mann, I. R.; Wygant, J. R.; Ergun, R. E.

    2016-09-01

    Waves with frequencies in the vicinity of the oxygen cyclotron frequency and its harmonics have been regularly observed on the Van Allen Probes satellites during geomagnetic storms. We focus on properties of these waves and present events from the main phase of two storms on 1 November 2012 and 17 March 2013 and associated dropouts of a few MeV electron fluxes. They are electromagnetic, in the frequency range ~0.5 to several Hz, and amplitude ~0.1 to a few nT in magnetic and ~0.1 to a few mV/m in electric field, with both the wave velocity and the Poynting vector directed almost parallel to the background magnetic field. These properties are very similar to those of electromagnetic ion cyclotron waves, which are believed to contribute to loss of ring current ions and radiation belt electrons and therefore can be also important for inner magnetosphere dynamics.

  11. Wave-driven butterfly distribution of Van Allen belt relativistic electrons.

    PubMed

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D N; Spence, H E; Funsten, H O; Blake, J B

    2015-10-05

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  12. Five Years of SETI with the Allen Telescope Array: Lessons Learned

    NASA Astrophysics Data System (ADS)

    Harp, Gerald

    2016-01-01

    We discuss recent observations at the Allen Telescope Array (ATA) supporting a wide ranging Search for Extraterrestrial Intelligence (SETI). The ATA supports observations over the frequency range 1-10 GHz with three simultaneous phased array beams used in an anticoincidence detector for false positive rejection. Here we summarize observational results over the years 2011-2015 covering multiple campaigns of exoplanet stars, the galactic plane, infrared excess targets, etc. Approximately 2 x 108 signals were identified and classified over more than 5000 hours of observation. From these results we consider various approaches to the rapid identification of human generated interference in the process of the search for a signal with origins outside the radius of the Moon's orbit. We conclude that the multi-beam technique is superb tool for answering the very difficult question of the direction of origin of signals. Data-based simulations of future instruments with more than 3 beams are compared.

  13. Convection Electric Field Observations by THEMIS and the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Califf, S.; Li, X.; Bonnell, J. W.; Wygant, J. R.; Malaspina, D.; Hartinger, M.; Thaller, S. A.

    2013-12-01

    We present direct electric field measurements made by THEMIS and the Van Allen Probes in the inner magnetosphere, focusing on the large-scale, near-DC convection electric field. The convection electric field drives plasma Earthward from the tail into the inner magnetosphere, playing a critical role in forming the ring current. Although it is normally shielded deep inside the magnetosphere, during storm times this large-scale electric field can penetrate to low L values (L < 3), eroding the plasmasphere and also providing a mechanism for ~100 keV electron injection into the slot region and inner radiation belt. The relationship of the convection electric field with the plasmasphere is also important for understanding the dynamic outer radiation belt, as the plasmapause boundary has been strongly correlated with the dynamic variation of the outer radiation belt electrons.

  14. Traveling wave solutions for bistable fractional Allen-Cahn equations with a pyramidal front

    NASA Astrophysics Data System (ADS)

    Chan, Hardy; Wei, Juncheng

    2017-05-01

    Using the method of sub-super-solution, we construct a solution of (- Δ) s u - cuz - f (u) = 0 on R3 of pyramidal shape. Here (- Δ) s is the fractional Laplacian of sub-critical order 1 / 2 < s < 1 and f is a bistable nonlinearity. Hence, the existence of a traveling wave solution for the parabolic fractional Allen-Cahn equation with pyramidal front is asserted. The maximum of planar traveling wave solutions in various directions gives a sub-solution. A super-solution is roughly defined as the one-dimensional profile composed with the signed distance to a rescaled mollified pyramid. In the main estimate we use an expansion of the fractional Laplacian in the Fermi coordinates.

  15. EMIC wave scale size in the inner magnetosphere: Observations from the dual Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Bonnell, J. W.; Agapitov, O.; Paulson, K.; Kletzing, C.

    2017-02-01

    Estimating the spatial scales of electromagnetic ion cyclotron (EMIC) waves is critical for quantifying their overall scattering efficiency and effects on thermal plasma, ring current, and radiation belt particles. Using measurements from the dual Van Allen Probes in 2013-2014, we characterize the spatial and temporal extents of regions of EMIC wave activity and how these depend on local time and radial distance within the inner magnetosphere. Observations are categorized into three types—waves observed by only one spacecraft, waves measured by both spacecraft simultaneously, and waves observed by both spacecraft with some time lag. Analysis reveals that dayside (and H+ band) EMIC waves more frequently span larger spatial areas, while nightside (and He+ band) waves are more often localized but can persist many hours. These investigations give insight into the nature of EMIC wave generation and support more accurate quantification of their effects on the ring current and outer radiation belt.

  16. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    NASA Astrophysics Data System (ADS)

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-10-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  17. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    PubMed Central

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons. PMID:26436770

  18. Van Allen Probe Explorations of Plasma Spatial and Temporal Scales in the Inner Magnetosphere

    NASA Astrophysics Data System (ADS)

    Niehof, J. T.; Larsen, B.; Skoug, R. M.; Reeves, G. D.; MacDonald, E.; Thomsen, M.; Funsten, H. O.; Friedel, R. H.

    2013-12-01

    We utilize the variable separation of the twin satellites of the Van Allen Probes mission to explore the time and spatial stability of plasma features in the inner magnetosphere. The spacecraft are in a leader-follower configuration with an approximately nine hour orbit, but with slightly different apogees and thus periods. Exploiting the resulting variation in separations, we survey differences in the plasma environment between inbound and outbound passes from a single satellite and between the two separated in time. The time separation ranges from minutes to 4.5 hours. From the HOPE instrument we obtain pitch angle resolved measurements of the plasma environment (for electrons, protons, helium, and oxygen). By utilizing both spacecraft, temporal and spatial effects are separated. By comparing temporal variations to drift and flow times, we determine which events' evolution is adequately described by simple flow or drift and which must result from more involved physics.

  19. Explaining occurrences of auroral kilometric radiation in Van Allen radiation belts

    NASA Astrophysics Data System (ADS)

    Xiao, Fuliang; Zhou, Qinghua; Su, Zhenpeng; He, Zhaoguo; Yang, Chang; Liu, Si; He, Yihua; Gao, Zhonglei

    2016-12-01

    Auroral kilometric radiation (AKR) is a strong terrestrial radio emission and dominates at higher latitudes because of reflection in vicinities of the source cavity and plasmapause. Recently, Van Allen Probes have observed occurrences of AKR emission in the equatorial region of Earth's radiation belts but its origin still remains an open question. Equatorial AKR can produce efficient acceleration of radiation belt electrons and is a risk to space weather. Here we report high-resolution observations during two small storm periods 4-6 April and 18-20 May 2013 and show, using a 3-D ray tracing simulation, that AKR can propagate downward all the way into the equatorial plane in the radiation belts under appropriate conditions. The simulated results can successfully explain the observed AKR's spatial distribution and frequency range, and the current results have a wide application to all other magnetized astrophysical objects in the universe.

  20. Variation of the ion composition in the ring current during magnetic storms: Van Allen Probes observations

    NASA Astrophysics Data System (ADS)

    Luo, Hao; Du, Aimin; Ge, Yasong; Cao, Xin; Zhang, Ying; Wang, Yuan

    2015-04-01

    It has been reported that the energy density of the oxygen ions in the ring current region will show more enhancements than protons during magnetic storms. Knowing how the ion composition changes during a magnetic storm is important for understanding the dynamic processes in the inner magnetosphere. By using ion flux data from HOPE and RBSPICE instruments on board the Van Allen probes, we study the energy density variation of both protons and oxygen ions during fifteen strong magnetic storms (minimum Dst < -80 nT) happened during year 2013 to 2014. Results provide important details about the ion composition at different storm stages and different magnetic local times. Results also give important indications about the ion acceleration in the inner magnetosphere and the source of the ring current ions during the magnetic storms.

  1. Van Allen Probes Empirical Model of the Plasma Environment Inside Geostationary Orbit

    NASA Astrophysics Data System (ADS)

    Larsen, B.; Reeves, G. D.; Friedel, R. H. W.; Thomsen, M. F.; Skoug, R. M.; Funsten, H. O.; MacDonald, E.

    2014-12-01

    With the Van Allen probes nearing a full precession around the Earth we present a parameterized empirical model of the plasma properties in the inner magnetosphere. Data from the Los Alamos National Laboratory built Helium-Oxygen-Proton-Electron (HOPE) spectrometer on this this unparalleled two-satellite mission provides excellent coverage of the equatorial magnetosphere inside of geostationary, albeit over a limited range of geomagnetic activity. Fusing data and derived products from the two spacecraft a specification of the state of the inner magnetosphere has been created providing species resolved fluxes, partial densities, temperatures, anisotropies, and ratios. This full coverage model reproduces some well know phenomenology and presents some lesser know behaviors providing new insights into details of plasma dynamics inside geostationary orbit.

  2. PIC Simulations of Banded Chorus Events from Van Allen Probes Observations

    NASA Astrophysics Data System (ADS)

    Fu, X.; Cowee, M.; Friedel, R. H.; Gary, S. P.; Hospodarsky, G. B.; Kletzing, C.; Liu, K.; MacDonald, E.; Reeves, G. D.; Skoug, R. M.; Winske, D.

    2013-12-01

    Banded chorus emissions are whistler waves with two bands separated by a narrow gap at 0.5ωce (ωce is the elctron gyro-frequency) in the frequency spectrum, often observed in the inner magnetosphere. The physical reason for the gap is still puzzling the space community. To better understand banded chorus generation, we identify occurrences of banded chorus in the Van Allen Probes EMFISIS data. Prameters derived from observations are used as initial conditions for our linear theory and nonlinear particle-in-cell simulations. By comparing our simulation results with electron pitch angle distributions from HOPE and wave spectra from EMFISIS, we will test some hypotheses for generation of banded chorus. LA-UR-13-26132.

  3. Recent Performance Testing Results Using the 3-element Production Test Array for the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Tarter, J. C.; Blitz, L.; ATA 25 person Team; Paul G. Allen Foundation Collaboration

    2002-12-01

    The Allen Telescope Array will consist of 350 fixed six-meter dishes at the Hat Creek Radio Observatory in northern California (land use permits pending). It is the first massively parallel array ever built. Where possible, components from consumer markets and mass-production manufacturing processes have been used to lower costs. The architecture of the array explicitly anticipates future growth as a result of "Moore's Law" improvements. There will be many novel features of this array including ultra-wideband instantaneous frequency coverage from 0.5 to 11 GHz, a very wide field of view (2.5 degrees across at 21 cm), miniaturized 80K cryogenics, full bandwidth analog data transmission from the antennas to the Myhrvold central processing facility, dynamic null-formation and tracking of satellite interferers, and continuous multi-user support for radio astronomical research and SETI explorations. Starting in July 2000, the technology development for this array has been a collaboration between the Paul G. Allen Foundation and the ATA team located at the SETI Institute and at the Radio Astronomy Laboratory at UC Berkeley. A rapid prototyping array (RPA) consisting of seven COTS antennas and room temperature L-band receivers was erected in Orinda, CA in March 2001. Thanks to strong and continuing support from Sun Microsystems, the RPA has provided an invaluable testbed for software development and evaluation of RFI mitigation schemes. An operational 3-element Production Test Array (PTA) has been implemented at Hat Creek Observatory over the last few months. The antennas, drives, monitor and control software, and frontend components are near-final versions to be manufactured for the full array. This poster provides performance data from the first few months of testing with the PTA. A final decision on commitment for construction is expected by April 1, 2003.

  4. Formation of the oxygen torus in the inner magnetosphere: Van Allen Probes observations

    DOE PAGES

    Nose, Masahito; Oimatsu, S.; Keika, K.; ...

    2015-02-19

    Here we study the formation process of an oxygen torus during the 12–15 November 2012 magnetic storm, using the magnetic field and plasma wave data obtained by Van Allen Probes. We estimate the local plasma mass density (ρL) and the local electron number density (neL) from the resonant frequencies of standing Alfvén waves and the upper hybrid resonance band. The average ion mass (M) can be calculated by M ~ ρL/neL under the assumption of quasi-neutrality of plasma. During the storm recovery phase, both Probe A and Probe B observe the oxygen torus at L = 3.0–4.0 and L =more » 3.7–4.5, respectively, on the morning side. The oxygen torus has M = 4.5–8 amu and extends around the plasmapause that is identified at L~3.2–3.9. We find that during the initial phase, M is 4–7 amu throughout the plasma trough and remains at ~1 amu in the plasmasphere, implying that ionospheric O+ ions are supplied into the inner magnetosphere already in the initial phase of the magnetic storm. Numerical calculation under a decrease of the convection electric field reveals that some of thermal O+ ions distributed throughout the plasma trough are trapped within the expanded plasmasphere, whereas some of them drift around the plasmapause on the dawnside. This creates the oxygen torus spreading near the plasmapause, which is consistent with the Van Allen Probes observations. We conclude that the oxygen torus identified in this study favors the formation scenario of supplying O+ in the inner magnetosphere during the initial phase and subsequent drift during the recovery phase.« less

  5. Generation and effects of EMIC waves observed by the Van Allen Probes on 18 March 2013

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Saikin, A.; Gamayunov, K. V.; Spence, H. E.; Larsen, B.; Geoffrey, R.; Smith, C. W.; Torbert, R. B.; Kurth, W. S.; Kletzing, C.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves play a crucial role in particle dynamics in the Earth's magnetosphere. The free energy for EMIC wave generation is usually provided by the temperature anisotropy of the energetic ring current ions. EMIC waves can in turn cause particle energization and losses through resonant wave-particle interactions. Using measurements from the Van Allen Probes, we perform a case study of EMIC waves and associated plasma conditions observed on 18 March 2013. From 0204 to 0211 UT, the Van Allen Probe-B detected He+-band EMIC wave activity in the post-midnight sector (MLT=4.6-4.9) at very low L-shells (L=2.6-2.9). The event occurred right outside the inward-pushed plasmapause in the early recovery phase of an intense geomagnetic storm - min. Dst = -132 nT at 2100 UT on 17 March 2013. During this event, the fluxes of energetic (> 1 keV), anisotropic O+ dominate both the H+ and He+ fluxes in this energy range. Meanwhile, O+ fluxes at low energies (< 0.1 keV) are low compared to H+ and He+ fluxes in the same energy range. The fluxes of <0.1 keV He+ are clearly enhanced during the wave event, indicating a signature of wave heating. To further confirm the association of the observed plasma features with the EMIC waves, we calculate the electron minimum resonant energy (Emin) and pitch angle diffusion coefficient (Dαα) of the EMIC wave packets by using nominal ion composition, derived total ion density from the frequencies of upper hybrid resonance, and measured ambient and wave magnetic field. EMIC wave growth rates are also calculated to evaluate the role of loss-cone distributed ring current ions in the EMIC wave generation.

  6. Pi2 Pulsations Observed by Van Allen Probes: A Case Study

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K. H.; Kwon, H. J.; Lee, D. H.; Kletzing, C.; Kurth, W. S.

    2014-12-01

    The plasmaspheric virtual resonance model has been proposed as one of the source mechanisms for low-latitude Pi2 pulsations. Few studies have used simultaneous multipoint observations in space to examine the spatial structure of Pi2 pulsations both inside and outside the plasmasphere. In this study we show multipoint observations for Pi2 pulsations using the Van Allen Probes (RBSP-A and RBSP-B). We focus on the two events that occurred between 1700 and 2000 UT on March 12, 2013, which were simultaneously observed by Van Allen Probes and Bohyun (BOH, L = 1.35) station in South Korea. By using plasma density measurements, we determined that during this time RBSP-A was located outside the plasmasphere and RBSP-B was located inside it. We found that the poloidal, radial (δBx) and compressional (δBz), magnetic field components, and the azimuthal (Ey) electric field component observed by both RBSP-A and RBSP-B have a high correlation with the H component at BOH for both events. The δBx and δBz oscillations at both RBSP-A and RBSP-B are nearly out of phase with ground Pi2. The Ey -H cross phases at RBSP-A outside the plasmapause and RBSP-B inside the plasmapause are nearly in quadrature for the first Pi2 event. These observations indicate that the Pi2 pulsations exist outside the plasmasphere with a radially standing signature which supports the plasmaspheric virtual resonance model.

  7. Formation of the oxygen torus in the inner magnetosphere: Van Allen Probes observations

    SciTech Connect

    Nose, Masahito; Oimatsu, S.; Keika, K.; Kletzing, C. A.; Kurth, W. S.; De Pascuale, S.; Smith, C. W.; MacDowall, R. J.; Reeves, Geoffrey D.; Nakano, S.; Spence, H. E.; Larsen, Brian Arthur

    2015-02-19

    Here we study the formation process of an oxygen torus during the 12–15 November 2012 magnetic storm, using the magnetic field and plasma wave data obtained by Van Allen Probes. We estimate the local plasma mass density (ρL) and the local electron number density (neL) from the resonant frequencies of standing Alfvén waves and the upper hybrid resonance band. The average ion mass (M) can be calculated by M ~ ρL/neL under the assumption of quasi-neutrality of plasma. During the storm recovery phase, both Probe A and Probe B observe the oxygen torus at L = 3.0–4.0 and L = 3.7–4.5, respectively, on the morning side. The oxygen torus has M = 4.5–8 amu and extends around the plasmapause that is identified at L~3.2–3.9. We find that during the initial phase, M is 4–7 amu throughout the plasma trough and remains at ~1 amu in the plasmasphere, implying that ionospheric O+ ions are supplied into the inner magnetosphere already in the initial phase of the magnetic storm. Numerical calculation under a decrease of the convection electric field reveals that some of thermal O+ ions distributed throughout the plasma trough are trapped within the expanded plasmasphere, whereas some of them drift around the plasmapause on the dawnside. This creates the oxygen torus spreading near the plasmapause, which is consistent with the Van Allen Probes observations. We conclude that the oxygen torus identified in this study favors the formation scenario of supplying O+ in the inner magnetosphere during the initial phase and subsequent drift during the recovery phase.

  8. New results from the Colorado CubeSat and comparison with Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Li, X.

    2013-05-01

    The Colorado Student Space Weather Experiment (CSSWE) is a 3-unit (10cm x 10cm x 30cm) CubeSat mission funded by the NSF, launched into a highly inclined (650) low-Earth (490km x 790km) orbit on 09/13/12 as a secondary payload under NASA's Educational Launch of Nanosatellites (ELaNa) program. CSSWE contains a single science payload, the Relativistic Electron and Proton Telescope integrated little experiment (REPTile), which is a simplified and miniaturized version of the Relativistic Electron and Proton Telescope (REPT) built at the Laboratory for Atmospheric and Space Physics (LASP) of University of Colorado for NASA/Van Allen Probes mission, which consists of two identical spacecraft, launched on 08/30/12, that traverse the heart of the radiation belts in a low inclination (100) orbit. REPTile is designed to measure the directional differential flux of protons ranging from 9 to 40 MeV and electrons from 0.5 to >3.3 MeV. Three-month science mission (full success) was completed on 1/05/13. We are now into the extended mission phase, focusing on data analysis and modeling. REPTile measures a fraction of the total population that has small enough equatorial pitch angles to reach the altitude of CSSWE, thus measuring the precipitating population as well as the trapped population. These measurements are critical for understanding the loss of outer radiation belt electrons. New results from CSSWE and comparison with Van Allen Probes data will be presented. The CSSWE is also an ideal class project, involving over 65 graduate and undergraduate students and providing training for the next generation of engineers and scientists over the full life-cycle of a satellite project.

  9. Analysis of Van Allen Probes Data Showing Nonlinear Electric Field Feedback During a Magnetic Storm

    NASA Astrophysics Data System (ADS)

    Liemohn, M. W.; Katus, R. M.; Smith, L. K.; Skoug, R. M.; Niehof, J. T.; Spence, H.; Wygant, J. R.; Bonnell, J. W.; Smith, C. W.; Kletzing, C.; Ilie, R.; Ganushkina, N.

    2013-12-01

    Van Allen Probes data was examined to assess the role of nonlinear feedback in relationship to the spatial structure of hot ions in the inner magnetosphere. During the magnetic storm that peaked on June 1, 2013, localized electric field perturbations from the EFW instrument were observed in relationship to the plasma pressure peak (as identified by the HOPE H+ and O+ fluxes in the 1-40 keV range, as well as magnetic field perturbations from EMFISIS) with a systematic sinusoidal perturbation. Near apogee, it takes the Van Allen Probes 30-60 minutes to traverse a peak in the ion fluxes. Therefore, the electric field was averaged over several minutes to remove the higher-frequency wave oscillations, revealing the longer-baseline perturbation associated with the pressure peak. While the fluxes indicate that the satellite is passing through a pressure peak, the magnetic field perturbation reveals the spatial location of the pressure extrema relative to the spacecraft location. The pattern of these electric fields relative to the location of the plasma pressure peak is in agreement with the hypothesis based on theory and numerical simulation results that an azimuthally localized pressure peak should create a systematic and predictable small-scale reconfiguration of the electric field. This electric field modification is because the field-aligned currents near each end of the pressure crescent close via Pedersen currents, perturbing the electric field in this region, as regulated by the ionospheric conductance. The level of this reconfiguration, relative to the expected dawn-dusk electric field within the magnetosphere, indicates the intensity of the nonlinear feedback.

  10. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot.

    PubMed

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B; Turkheimer, Federico E

    2016-04-15

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  11. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot

    PubMed Central

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B.; Turkheimer, Federico E.

    2016-01-01

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  12. BNL ATLAS Grid Computing

    ScienceCinema

    Michael Ernst

    2016-07-12

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  13. Language Industries Atlas.

    ERIC Educational Resources Information Center

    Hearn, P. M., Ed.; Button, D. F., Ed.

    This atlas describes the activities of public and private organizations that create the infrastructure within which languages are able to develop and interact in the European Community (EC). It contains over 1,000 descriptions of activities that play a role in shaping the language industries, from a user or provider perspective. The atlas is…

  14. BNL ATLAS Grid Computing

    SciTech Connect

    Michael Ernst

    2008-10-02

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  15. A population-average MRI-based atlas collection of the rhesus macaque.

    PubMed

    McLaren, Donald G; Kosmatka, Kristopher J; Oakes, Terrance R; Kroenke, Christopher D; Kohama, Steven G; Matochik, John A; Ingram, Don K; Johnson, Sterling C

    2009-03-01

    Magnetic resonance imaging (MRI) studies of non-human primates are becoming increasingly common; however, the well-developed voxel-based methodologies used in human studies are not readily applied to non-human primates. In the present study, we create a population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to creating a publicly available T1-weighted atlas (http://www.brainmap.wisc.edu/monkey.html), probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem, K.S. and Logothetis, N.K. (2006) atlas providing an explicit link to histological sections. Additionally, we have created a transform to integrate these atlases with the F99 surface-based atlas in CARET. It is anticipated that these tools will help facilitate voxel-based imaging methodologies in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.

  16. Quantitative evaluation of registration methods for atlas-based diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Wu, Xue; Eggebrecht, Adam T.; Culver, Joseph P.; Zhan, Yuxuan; Basevi, Hector; Dehghani, Hamid

    2013-06-01

    In Diffuse Optical Tomography (DOT), an atlas-based model can be used as an alternative to a subject-specific anatomical model for recovery of brain activity. The main step of the generation of atlas-based subject model is the registration of atlas model to the subject head. The accuracy of the DOT then relies on the accuracy of registration method. In this work, 11 registration methods are quantitatively evaluated. The registration method with EEG 10/20 systems with 19 landmarks and non-iterative point to point algorithm provides approximately 1.4 mm surface error and is considered as the most efficient registration method.

  17. A Glimpse of Atlas

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Saturn's little moon Atlas orbits Saturn between the outer edge of the A ring and the fascinating, twisted F ring. This image just barely resolves the disk of Atlas, and also shows some of the knotted structure for which the F ring is known. Atlas is 32 kilometers (20 miles) across.

    The bright outer edge of the A ring is overexposed here, but farther down the image several bright ring features can be seen.

    The image was taken in visible light with the Cassini spacecraft narrow-angle camera on April 25, 2005, at a distance of approximately 2.4 million kilometers (1.5 million miles) from Atlas and at a Sun-Atlas-spacecraft, or phase, angle of 60 degrees. Resolution in the original image was 14 kilometers (9 miles) per pixel.

  18. National Atlas maps

    USGS Publications Warehouse

    ,

    1991-01-01

    The National Atlas of the United States of America was published by the U.S. Geological Survey in 1970. Its 765 maps and charts are on 335 14- by 19-inch pages. Many of the maps span facing pages. It's worth a quick trip to the library just to leaf through all 335 pages of this book. Rapid scanning of its thematic maps yields rich insights to the geography of issues of continuing national interest. On most maps, the geographic patterns are still valid, though the data are not current. The atlas is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. The maps dated after 1970 are either revisions of original atlas maps, or new maps published in atlas format. The titles of the separate maps are listed here.

  19. A cross-validated cytoarchitectonic atlas of the human ventral visual stream.

    PubMed

    Rosenke, M; Weiner, K S; Barnett, M A; Zilles, K; Amunts, K; Goebel, R; Grill-Spector, K

    2017-02-14

    The human ventral visual stream consists of several areas considered processing stages essential for perception and recognition. A fundamental microanatomical feature differentiating areas is cytoarchitecture, which refers to the distribution, size, and density of cells across cortical layers. Because cytoarchitectonic structure is measured in 20-micron-thick histological slices of postmortem tissue, it is difficult to assess (a) how anatomically consistent these areas are across brains and (b) how they relate to brain parcellations obtained with prevalent neuroimaging methods, acquired at the millimeter and centimeter scale. Therefore, the goal of this study was to (a) generate a cross-validated cytoarchitectonic atlas of the human ventral visual stream on a whole brain template that is commonly used in neuroimaging studies and (b) to compare this atlas to a recently published retinotopic parcellation of visual cortex (Wang, 2014). To achieve this goal, we generated an atlas of eight cytoarchitectonic areas: four areas in the occipital lobe (hOc1-hOc4v) and four in the fusiform gyrus (FG1-FG4) and tested how alignment technique affects the accuracy of the atlas. Results show that both cortex-based alignment (CBA) and nonlinear volumetric alignment (NVA) generate an atlas with better cross-validation performance than affine volumetric alignment (AVA). Additionally, CBA outperformed NVA in 6/8 of the cytoarchitectonic areas. Finally, the comparison of the cytoarchitectonic atlas to a retinotopic atlas shows a clear correspondence between cytoarchitectonic and retinotopic areas in the ventral visual stream. The successful performance of CBA suggests a coupling between cytoarchitectonic areas and macroanatomical landmarks in the human ventral visual stream, and furthermore that this coupling can be utilized towards generating an accurate group atlas. In addition, the coupling between cytoarchitecture and retinotopy highlights the potential use of this atlas in

  20. Van Allen Probes Mission Space Academy: Educating middle school students about Earth's mysterious radiation belts

    NASA Astrophysics Data System (ADS)

    Butler, L.; Turney, D.; Matiella Novak, A.; Smith, D.; Simon, M.

    2013-12-01

    How's the weather in space? Why on Earth did NASA send two satellites above Earth to study radiation belts and space weather? To learn the answer to questions about NASA's Van Allen Probes mission, 450 students and their teachers from Maryland middle schools attended Space Academy events highlighting the Van Allen Probes mission. Sponsored by the Applied Physics Laboratory (APL) and Discovery Education, the events are held at the APL campus in Laurel, MD. Space Academies take students and teachers on behind-the-scenes exploration of how spacecraft are built, what they are designed to study, and introduces them to the many professionals that work together to create some of NASA's most exciting projects. Moderated by a public relations representative in the format of an official NASA press conference, the daylong event includes a student press conference with students as reporters and mission experts as panelists. Lunch with mission team members gives students a chance to ask more questions. After lunch, students don souvenir clean room suits, enjoy interactive science demonstrations, and tour APL facilities where the Van Allen Probes were built and tested before launch. Students may even have an opportunity to peek inside a clean room to view spacecraft being assembled. Prior to the event, teachers are provided with classroom activities, lesson plans, and videos developed by APL and Discovery Education to help prepare students for the featured mission. The activities are aligned to National Science Education Standards and appropriate for use in the classroom. Following their visit, student journalists are encouraged to write a short article about their field trip; selections are posted on the Space Academy web site. Designed to engage, inspire, and influence attitudes about space science and STEM careers, Space Academies provide an opportunity to attract underserved populations and emphasize that space science is for everyone. Exposing students to a diverse group of

  1. Simultaneous Pi2 observations by the Van Allen Probes inside and outside the plasmasphere

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K.-H.; Kwon, H.-J.; Lee, D.-H.; Park, J.-S.; Choi, J.; Hyun, K.; Kurth, W. S.; Kletzing, C.; Wygant, J. R.; Huang, J.

    2015-06-01

    Plasmaspheric virtual resonance (PVR) model has been proposed as one of source mechanisms for low-latitude Pi2 pulsations. Since PVR-associated Pi2 pulsations are not localized inside the plasmasphere, simultaneous multipoint observations inside and outside the plasmasphere require to test the PVR model. Until now, however, there are few studies using simultaneous multisatellite observations inside and outside the plasmasphere for understanding the radial structure of Pi2 pulsation. In this study, we focus on the Pi2 event observed at low-latitude Bohyun (BOH, L = 1.35) ground station in South Korea in the postmidnight sector (magnetic local time (MLT) = 3.0) for the interval from 1730 to 1900 UT on 12 March 2013. By using electron density derived from the frequency of the upper hybrid waves detected at Van Allen Probe-A (VAP-A) and Van Allen Probe-B (VAP-B), the plasmapause is identified. At the time of the Pi2 event, VAP-A was outside the plasmasphere near midnight (00:55 MLT and L =˜ 6), while VAP-B was inside the plasmasphere in the postmidnight sector (02:15 MLT and L =˜ 5). VAP-B observed oscillations in the compressional magnetic field component (Bz) and the dawn-to-dusk electric field component (Ey), having high coherence with the BOH Pi2 pulsation in the H component. The H-Bz and H-Ey cross phases at VAP-B inside the plasmasphere were near -180° and -90°, respectively. These phase relationships among Bz, Ey, and H are consistent with a radially standing oscillation of the fundamental mode reported in previous studies. At VAP-A outside the plasmasphere, Bz oscillations were highly correlated with BOH Pi2 pulsations with ˜-180° phase delay, and the H-Ey cross phase is near -90°. From these two-satellite observations, we suggest that the fundamental PVR mode is directly detected by VAP-A and VAP-B.

  2. MRIVIEW: An interactive computational tool for investigation of brain structure and function

    SciTech Connect

    Ranken, D.; George, J.

    1993-12-31

    MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

  3. The Millennium Star Atlas

    NASA Astrophysics Data System (ADS)

    Sinnott, R. W.

    1997-08-01

    Derived from Hipparcos and Tycho observations, the Millennium Star Atlas is a set of 1548 charts covering the entire sky to about magnitude 11. It stands apart from all previous printed atlases in completeness to magnitude 10 and in uniformity around the sky. The generous chart scale has made possible a number of innovations never before seen in a star atlas: arrows on high-proper-motion stars, double-star ticks conveying separation and position angle for a specific modern epoch, distance labels for nearby stars, and variable stars coded by amplitude, period, and type. Among the nonstellar objects plotted, more than 8000 galaxies are shown with aspect ratio and orientation.

  4. Deformation-based brain morphometry in rats.

    PubMed

    Gaser, Christian; Schmidt, Silvio; Metzler, Martin; Herrmann, Karl-Heinz; Krumbein, Ines; Reichenbach, Jürgen R; Witte, Otto W

    2012-10-15

    Magnetic resonance imaging (MRI)-based morphometry provides in vivo evidence for macro-structural plasticity of the brain. Experiments on small animals using automated morphometric methods usually require expensive measurements with ultra-high field dedicated animal MRI systems. Here, we developed a novel deformation-based morphometry (DBM) tool for automated analyses of rat brain images measured on a 3-Tesla clinical whole body scanner with appropriate coils. A landmark-based transformation of our customized reference brain into the coordinates of the widely used rat brain atlas from Paxinos and Watson (Paxinos Atlas) guarantees the comparability of results to other studies. For cross-sectional data, we warped images onto the reference brain using the low-dimensional nonlinear registration implemented in the MATLAB software package SPM8. For the analysis of longitudinal data sets, we chose high-dimensional registrations of all images of one data set to the first baseline image which facilitate the identification of more subtle structural changes. Because all deformations were finally used to transform the data into the space of the Paxinos Atlas, Jacobian determinants could be used to estimate absolute local volumes of predefined regions-of-interest. Pilot experiments were performed to analyze brain structural changes due to aging or photothrombotically-induced cortical stroke. The results support the utility of DBM based on commonly available clinical whole-body scanners for highly sensitive morphometric studies on rats.

  5. An extreme distortion of the Van Allen belt arising from the 'Hallowe'en' solar storm in 2003.

    PubMed

    Baker, D N; Kanekal, S G; Li, X; Monk, S P; Goldstein, J; Burch, J L

    2004-12-16

    The Earth's radiation belts--also known as the Van Allen belts--contain high-energy electrons trapped on magnetic field lines. The centre of the outer belt is usually 20,000-25,000 km from Earth. The region between the belts is normally devoid of particles, and is accordingly favoured as a location for spacecraft operation because of the benign environment. Here we report that the outer Van Allen belt was compressed dramatically by a solar storm known as the 'Hallowe'en storm' of 2003. From 1 to 10 November, the outer belt had its centre only approximately 10,000 km from Earth's equatorial surface, and the plasmasphere was similarly displaced inwards. The region between the belts became the location of high particle radiation intensity. This remarkable deformation of the entire magnetosphere implies surprisingly powerful acceleration and loss processes deep within the magnetosphere.

  6. The role of ring current particle injections: Global simulations and Van Allen Probes observations during 17 March 2013 storm

    NASA Astrophysics Data System (ADS)

    Yu, Yiqun; Jordanova, Vania; Welling, Dan; Larsen, Brian; Claudepierre, Seth G.; Kletzing, Craig

    2014-02-01

    We simulate substorm injections observed by the Van Allen Probes during the 17 March 2013 storm using a self-consistent coupling between the ring current model RAM-SCB and the global MHD model BATS-R-US. This is a significant advancement compared to previous studies that used artificially imposed electromagnetic field pulses to mimic substorm dipolarization and associated inductive electric field. Several substorm dipolarizations and injections are reproduced in the MHD model, in agreement with the timing of shape changes in the AE/AL index. The associated inductive electric field transports plasma sheet plasma to geostationary altitudes, providing the boundary plasma source to the ring current model. It is found that impulsive plasma sheet injections, together with a large-scale convection electric field, are necessary to develop a strong ring current. Comparisons with Van Allen Probes observations show that our model reasonably well captures dispersed electron injections and the global Dst index.

  7. Learning to rank atlases for multiple-atlas segmentation.

    PubMed

    Sanroma, Gerard; Wu, Guorong; Gao, Yaozong; Shen, Dinggang

    2014-10-01

    Recently, multiple-atlas segmentation (MAS) has achieved a great success in the medical imaging area. The key assumption is that multiple atlases have greater chances of correctly labeling a target image than a single atlas. However, the problem of atlas selection still remains unexplored. Traditionally, image similarity is used to select a set of atlases. Unfortunately, this heuristic criterion is not necessarily related to the final segmentation performance. To solve this seemingly simple but critical problem, we propose a learning-based atlas selection method to pick up the best atlases that would lead to a more accurate segmentation. Our main idea is to learn the relationship between the pairwise appearance of observed instances (i.e., a pair of atlas and target images) and their final labeling performance (e.g., using the Dice ratio). In this way, we select the best atlases based on their expected labeling accuracy. Our atlas selection method is general enough to be integrated with any existing MAS method. We show the advantages of our atlas selection method in an extensive experimental evaluation in the ADNI, SATA, IXI, and LONI LPBA40 datasets. As shown in the experiments, our method can boost the performance of three widely used MAS methods, outperforming other learning-based and image-similarity-based atlas selection methods.

  8. Learning to Rank Atlases for Multiple-Atlas Segmentation

    PubMed Central

    Sanroma, Gerard; Wu, Guorong; Gao, Yaozong

    2014-01-01

    Recently, multiple-atlas segmentation (MAS) has achieved a great success in the medical imaging area. The key assumption is that multiple atlases have greater chances of correctly labeling a target image than a single atlas. However, the problem of atlas selection still remains unexplored. Traditionally, image similarity is used to select a set of atlases. Unfortunately, this heuristic criterion is not necessarily related to the final segmentation performance. To solve this seemingly simple but critical problem, we propose a learning-based atlas selection method to pick up the best atlases that would lead to a more accurate segmentation. Our main idea is to learn the relationship between the pairwise appearance of observed instances (i.e., a pair of atlas and target images) and their final labeling performance (e.g., using the Dice ratio). In this way, we select the best atlases based on their expected labeling accuracy. Our atlas selection method is general enough to be integrated with any existing MAS method. We show the advantages of our atlas selection method in an extensive experimental evaluation in the ADNI, SATA, IXI, and LONI LPBA40 datasets. As shown in the experiments, our method can boost the performance of three widely used MAS methods, outperforming other learning-based and image-similarity-based atlas selection methods. PMID:24893367

  9. 77 FR 48960 - Foreign-Trade Zone 12-McAllen, TX Notification of Proposed Export Production Activity TST NA Trim...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-15

    ... Activity TST NA Trim, LLC (Fabric/Leather Lamination and Cutting) Hidalgo, TX The McAllen Foreign Trade... TST NA Trim, LLC (TST), located in Hidalgo, Texas. The notification conforming to the requirements...

  10. The Global Positioning System constellation as a space weather monitor. Comparison of electron measurements with Van Allen Probes data

    DOE PAGES

    Morley, Steven K.; Sullivan, John P.; Henderson, Michael G.; ...

    2016-02-06

    Energetic electron observations in Earth's radiation belts are typically sparse, and multipoint studies often rely on serendipitous conjunctions. This paper establishes the scientific utility of the Combined X-ray Dosimeter (CXD), currently flown on 19 satellites in the Global Positioning System (GPS) constellation, by cross-calibrating energetic electron measurements against data from the Van Allen Probes. By breaking our cross calibration into two parts—one that removes any spectral assumptions from the CXD flux calculation and one that compares the energy spectra—we first validate the modeled instrument response functions, then the calculated electron fluxes. Unlike previous forward modeling of energetic electron spectra, wemore » use a combination of four distributions that together capture a wide range of observed spectral shapes. Moreover, our two-step approach allowed us to identify, and correct for, small systematic offsets between block IIR and IIF satellites. Using the Magnetic Electron Ion Spectrometer and Relativistic Electron-Proton Telescope on Van Allen Probes as a “gold standard,” here we demonstrate that the CXD instruments are well understood. A robust statistical analysis shows that CXD and Van Allen Probes fluxes are similar and the measured fluxes from CXD are typically within a factor of 2 of Van Allen Probes at energies inline image4 MeV. Our team present data from 17 CXD-equipped GPS satellites covering the 2015 “St. Patrick's Day” geomagnetic storm to illustrate the scientific applications of such a high data density satellite constellation and therefore demonstrate that the GPS constellation is positioned to enable new insights in inner magnetospheric physics and space weather forecasting.« less

  11. A Useful Allene for the Stereoselective Synthesis of Protected Quaternary 2-Amino-2-vinyl-1,3-diols.

    PubMed

    Rodríguez, Aleix; Ariza, Xavier; Contreras, Miguel A; Garcia, Jordi; Lloyd-Williams, Paul; Mercadal, Nerea; Sánchez, Carolina

    2017-02-03

    Treatment of readily available allene 1 with Cy2BH followed by addition of an aldehyde led to quaternary protected 2-amino-2-vinyl-1,3-diols in high yield and excellent stereochemical purity. The choice of benzoyl as N-protecting group is critical since the observed N- to O-Bz transfer during the process prevents later undesired isomerizations in the adducts and keeps all heteroatoms protected.

  12. Enantioselective Generation of Adjacent Stereocenters in a Copper‐Catalyzed Three‐Component Coupling of Imines, Allenes, and Diboranes

    PubMed Central

    Yeung, Kay; Ruscoe, Rebecca E.; Rae, James; Pulis, Alexander P.

    2016-01-01

    Abstract A highly enantio‐ and diastereoselective copper‐catalyzed three‐component coupling affords the first general synthesis of homoallylic amines bearing adjacent stereocenters from achiral starting materials. The method utilizes a commercially available NHC ligand and copper source, operates at ambient temperature, couples readily available simple imines, allenes, and diboranes, and yields high‐value homoallylic amines that exhibit versatile amino, alkenyl, and boryl units. PMID:27539673

  13. The Global Positioning System constellation as a space weather monitor. Comparison of electron measurements with Van Allen Probes data

    SciTech Connect

    Morley, Steven K.; Sullivan, John P.; Henderson, Michael G.; Blake, J. Bernard; Baker, Daniel N.

    2016-02-06

    Energetic electron observations in Earth's radiation belts are typically sparse, and multipoint studies often rely on serendipitous conjunctions. This paper establishes the scientific utility of the Combined X-ray Dosimeter (CXD), currently flown on 19 satellites in the Global Positioning System (GPS) constellation, by cross-calibrating energetic electron measurements against data from the Van Allen Probes. By breaking our cross calibration into two parts—one that removes any spectral assumptions from the CXD flux calculation and one that compares the energy spectra—we first validate the modeled instrument response functions, then the calculated electron fluxes. Unlike previous forward modeling of energetic electron spectra, we use a combination of four distributions that together capture a wide range of observed spectral shapes. Moreover, our two-step approach allowed us to identify, and correct for, small systematic offsets between block IIR and IIF satellites. Using the Magnetic Electron Ion Spectrometer and Relativistic Electron-Proton Telescope on Van Allen Probes as a “gold standard,” here we demonstrate that the CXD instruments are well understood. A robust statistical analysis shows that CXD and Van Allen Probes fluxes are similar and the measured fluxes from CXD are typically within a factor of 2 of Van Allen Probes at energies inline image4 MeV. Our team present data from 17 CXD-equipped GPS satellites covering the 2015 “St. Patrick's Day” geomagnetic storm to illustrate the scientific applications of such a high data density satellite constellation and therefore demonstrate that the GPS constellation is positioned to enable new insights in inner magnetospheric physics and space weather forecasting.

  14. Allen's big-eared bat (Idionycteris phyllotis) documented in colorado based on recordings of its distinctive echolocation call

    USGS Publications Warehouse

    Hayes, M.A.; Navo, K.W.; Bonewell, L.; Mosch, C.J.; Adams, R.A.

    2009-01-01

    Allen's big-eared bat (Idionycteris phyllotis) inhabits much of the southwestern USA, but has not been documented in Colorado. We recorded echolocation calls consistent with I. phyllotis near La Sal Creek, Montrose County, Colorado. Based on characteristics of echolocation calls and flight behavior, we conclude that the echolocation calls described here were emitted by I. phyllotis and that they represent the first documentation of this species in Colorado.

  15. Van Allen Probes ECT/MagEIS Background Corrected Electron Flux Measurements: Methods and Initial Findings

    NASA Astrophysics Data System (ADS)

    Claudepierre, S. G.; O'Brien, T. P., III; Blake, J. B.; Fennell, J.; Looper, M. D.; Clemmons, J. H.; Roeder, J. L.; Mazur, J. E.; Mulligan, T. L.

    2014-12-01

    We present results from the Magnetic Electron Ion Spectrometer (MagEIS) instrument, part ofthe Energetic Composition and Thermal Plasma (ECT) Suite, onboard the NASA Van AllenProbes spacecraft. The ECT/MagEIS instrument measures radiation belt electrons in the ~20-4000 keV energy range and protons in the ~60-1000 keV energy range, with high resolution inboth energy and pitch-angle. In addition, the MagEIS electron measurement technique allowsfor a full quantification of the source(s) of background contamination in the measurement.MagEIS is thus able to make clean, reliable electron flux observations in the presence of strongpenetrating backgrounds, for example, contamination from relativistic protons in the inner zoneand inner slot region. We summarize our background correction algorithm, describe the varioussources of background contamination, and present an overview of our initial findings using thebackground corrected data set. Understanding the causes and effects of backgroundcontamination in the MagEIS electron data set is crucial for the interpretation and proper use ofsuch data. The techniques described will facilitate new investigations into the dynamics of theEarth's electron radiation belts, which have thus far not been possible.

  16. Automated Determination of Electron Density from Electric Field Measurements on the Van Allen Probes Spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, I. S.; Spasojevic, M.; Shprits, Y.

    2015-12-01

    In this study we present an algorithm for automatic inference of the electron number density from plasma wave measurement made onboard NASA's Van Allen Probes mission. It accomplishes this by using feedforward neural networks to automatically infer the upper hybrid resonance frequency, 𝑓𝑢h𝑟, from plasma wave measurement, which is then used to determine the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detection (Kurth et al. [JGR, 2014]). We describe the design and implementation of the algorithm, as well as the resulting electron number density distribution. Resulting densities are compared with the densities obtained by Kurth et al. [JGR, 2014] and also to the empirical plasmasphere and trough density model of Sheeley et al. [JGR, 2001]. The analysis of the conditions, under which densities obtained by the proposed method differ significantly from the model of Sheeley et al. [JGR, 2001], is presented. Finally, we discuss the dependence of the electron number density on magnetic activity (Kp) and magnetic local time.

  17. Inner magnetosphere plasma, statistics from the Van Allen Probes HOPE instrument and data release 3.

    NASA Astrophysics Data System (ADS)

    Larsen, B.; Skoug, R. M.; Olson, D. K.; Reeves, G.; Friedel, R. H.; Funsten, H. O.

    2015-12-01

    As the twin Van Allen probes spacecraft complete three years on-orbit more than a complete revolution in local time has occurred. We present the state of the HOPE plasma data and statistics of the plasma distribution inside of geostationary orbit. Over the course of the mission a better understanding of the instrument has been gained and the needed corrections added to the data to enable long-term statistics to be collected and compared with confidence. The major correction to the data is the expected degradation of the channel electron multiplier (CEM) efficiency as a function of time and count rate. HOPE provides background data sufficient to monitor the absolute detection efficiency throughout the mission. We have incorporated a time dependent gain correction factor to the data that normalizes the gain and thus the derived plasma properties. In addition the CEM bias voltage was adjusted bringing the gain back toward launch values. With a standard set of data electron and ion composition statistics are computed and presented. These statistics serve as a L-MLT dependent distribution to begin inner magnetosphere plasma modeling, instrument comparison, and climatology studies. These data are presented as ECT HOPE release 3.

  18. Inner magnetosphere plasma, statistics from the Van Allen Probes HOPE instrument and data release 3.

    NASA Astrophysics Data System (ADS)

    Lotko, W.; Smith, R. H.; Zhang, B.; Ouellette, J.; Brambles, O.; Lyon, J.; Wiltberger, M. J.

    2014-12-01

    As the twin Van Allen probes spacecraft complete three years on-orbit more than a complete revolution in local time has occurred. We present the state of the HOPE plasma data and statistics of the plasma distribution inside of geostationary orbit. Over the course of the mission a better understanding of the instrument has been gained and the needed corrections added to the data to enable long-term statistics to be collected and compared with confidence. The major correction to the data is the expected degradation of the channel electron multiplier (CEM) efficiency as a function of time and count rate. HOPE provides background data sufficient to monitor the absolute detection efficiency throughout the mission. We have incorporated a time dependent gain correction factor to the data that normalizes the gain and thus the derived plasma properties. In addition the CEM bias voltage was adjusted bringing the gain back toward launch values. With a standard set of data electron and ion composition statistics are computed and presented. These statistics serve as a L-MLT dependent distribution to begin inner magnetosphere plasma modeling, instrument comparison, and climatology studies. These data are presented as ECT HOPE release 3.

  19. Comparison between Low and High Latitude Lightning VLF Wave Propagation Using WWLLN and Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Holzworth, R. H., II; Brundell, J. B.; Wygant, J. R.; Hospodarsky, G. B.; Mozer, F.; Jacobson, A. R.; Bonnell, J. W.

    2014-12-01

    Lightning produces strong broadband radio waves, called "sferics", which propagate in the Earth-ionosphere waveguide and are detected thousands of kilometers away from their source. Global real-time detection of lightning strokes including their time, location and energy, is conducted with the World Wide Lightning Location Network (WWLLN). In the ionosphere, these sferics couple into very low frequency (VLF) whistler waves which propagate obliquely to the Earth's magnetic field. Possible one-to-one coincidence between lightning and VLF whistler wave is already found by the conjunction work between WWLLN and Van Allen Probes (formerly known as the Radiation Belt Storm Probes (RBSP)). The previous global study showed a good match between WWLLN sferics and RBSP VLF whistlers at low L shell region (L < 3). In this summer, we started obtaining high sampling mode data from RBSP near the apogee. Initial results indicate many one-to-one coincidences at high L shell region (L>4). The whistlers observed at high L shell region are often nose whistlers. In our work, we will show the statistics results between WWLLN sferics and RBSP VLF whistlers at high L shell region. This talk will also explore the difference between low and high latitude lightning VLF wave propagation.

  20. Revealing the generation of extremely low frequency chorus in Van Allen radiation belts

    DOE PAGES

    Xiao, Fuliang; Liu, Si; Tao, Xin; ...

    2017-03-02

    Recent studies have shown that chorus can efficiently accelerate the outer radiation belt electrons to relativistic energies. Chorus, previously often observed above 0.1 equatorial electron gyrofrequency fce, was generated by energetic electrons originating from Earth's plasmasheet. Chorus below 0.1 fce has seldom been reported until the recent data from Van Allen Probes but its origin has not been revealed so far. Because electron resonant energy can approach the relativistic level at extremely low frequency relativistic effects should be considered in the formula for whistler-mode wave growth rate. Here we report high-resolution observations during the 14 October 2014 small storm andmore » firstly demonstrate, using a fully relativistic simulation, that electrons with the high energy tail population and relativistic pitch angle anisotropy can provide free energy sufficient for generating chorus below 0.1 fce. The simulated wave growth displays a very similar pattern to the observations. Finally, the current results can be applied to Jupiter, Saturn and other magnetized planets.« less

  1. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    DOE PAGES

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; ...

    2015-10-05

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth’s magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28more » June 2013 geomagnetic storm. In conclusion, simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. Finally, the current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.« less

  2. Understanding Earth's radiation belt electron dynamics: Van Allen Probes observations and simulations

    NASA Astrophysics Data System (ADS)

    Li, Wen; Ma, Qianli; Thorne, Richard; Bortnik, Jacob; Zhang, Xiaojia

    2016-10-01

    Various physical processes are known to cause acceleration, loss, and transport of energetic electrons in the Earth's radiation belts, but their quantitative roles in different time and space need further investigation. In the present paper, we evaluate the relative roles of various physical processes during geomagnetic storms using a 3D diffusion simulation. By quantitatively comparing the electron evolution observed by Van Allen Probes and simulation, we found that whistler-mode chorus waves play a critical role in accelerating electrons up to several MeV through efficient energy diffusion. By only including radial diffusion driven by ultra-low-frequency waves, the simulation underestimates the observed electron acceleration, while radial diffusion plays an important role in redistributing electrons. Although an additional loss process is required to fully explain the overestimated electron fluxes at multi-MeV, the combined physical processes of radial diffusion and scattering by whistler-mode waves reproduce the observed electron dynamics remarkably well, suggesting that quasi-linear diffusion theory is reasonable to evaluate radiation belt electron dynamics, and the importance of nonlinear wave-particle interaction may still remain as an open question. We would like to acknowledge AFOSR Award FA9550-15-1-0158, NASA Grants NNX15AI96G, NNX15AF61G, and the NSF Grant AGS 1564510 for supporting this research.

  3. A long-lived relativistic electron storage ring embedded in Earth's outer Van Allen belt.

    PubMed

    Baker, D N; Kanekal, S G; Hoxie, V C; Henderson, M G; Li, X; Spence, H E; Elkington, S R; Friedel, R H W; Goldstein, J; Hudson, M K; Reeves, G D; Thorne, R M; Kletzing, C A; Claudepierre, S G

    2013-04-12

    Since their discovery more than 50 years ago, Earth's Van Allen radiation belts have been considered to consist of two distinct zones of trapped, highly energetic charged particles. The outer zone is composed predominantly of megaelectron volt (MeV) electrons that wax and wane in intensity on time scales ranging from hours to days, depending primarily on external forcing by the solar wind. The spatially separated inner zone is composed of commingled high-energy electrons and very energetic positive ions (mostly protons), the latter being stable in intensity levels over years to decades. In situ energy-specific and temporally resolved spacecraft observations reveal an isolated third ring, or torus, of high-energy (>2 MeV) electrons that formed on 2 September 2012 and persisted largely unchanged in the geocentric radial range of 3.0 to ~3.5 Earth radii for more than 4 weeks before being disrupted (and virtually annihilated) by a powerful interplanetary shock wave passage.

  4. Estimates of trapped radiation encountered on low-thrust trajectories through the Van Allen belts

    NASA Technical Reports Server (NTRS)

    Karp, I. M.

    1973-01-01

    Estimates were made of the number of trapped protons and electrons encountered by vehicles on low-thrust trajectories through the Van Allen belts. The estimates serve as a first step in assessing whether these radiations present a problem to on-board sensitive components and payload. The integrated proton spectra and electron spectra are presented for the case of a trajectory described by a vehicle with a constant-thrust acceleration A sub c equal to 0.001 meter/sq sec. This value of acceleration corresponds to a trip time of about 54 days from low earth orbit to synchronous orbit. It is shown that the time spent in the belts and hence the radiation encountered vary nearly inversely with the value of thrust acceleration. Thus, the integrated spectral values presented for the case of A sub c = 0.001 meter/sq sec can be generalized for any other value of thrust acceleration by multiplying them by the factor 0.001/A sub c.

  5. The seasonal dependence of relativistic electron fluxes in the Earth's outer van Allen Belt

    NASA Astrophysics Data System (ADS)

    Kanekal, S. G.; Baker, D. N.; McPherron, R.

    2007-12-01

    It is well known that geomagnetic activity shows a marked seasonal dependence. This effect has been attributed to the seasonal variation of the Earth's dipole tilt angle exposing the magnetosphere to an increased southward component of the interplanetary field (the Russell-McPherron effect) or an increased solar wind velocity (the axial/equinoctial effect). We examine the seasonal dependence of relativistic electron fluxes in the Earth's outer Van Allen belt. An earlier investigation by Baker et. al., (1999) found that the relativistic electron fluxes do show a strong seasonal dependence with the equinoctial electron fluxes being almost three times higher than the solstitial fluxes. We extend this previous investigation using data obtained by sensors onboard SAMPEX. This study of the seasonal dependence is based on data with a higher time resolution as compared to the earlier study. The results of our analysis show that the peak electron fluxes are shifted in time from the nominal equinoctial times. We discuss some possible implications of our observations in the context of electron energization in the Earth's magnetosphere. Baker, D.N., S.G. Kanekal, T.I. Pulkkinen, and J.B. Blake, Equinoctial and solstitial averages of magnetospheric relativistic electrons: A strong semiannual modulation, Geophys. Res. Lett., 26, No. 20, 3193-3196, 1999.

  6. Aromatic Osmacyclopropenefuran Bicycles and Their Relevance for the Metal-Mediated Hydration of Functionalized Allenes.

    PubMed

    Batuecas, María; Castro-Rodrigo, Ruth; Esteruelas, Miguel A; García-Yebra, Cristina; López, Ana M; Oñate, Enrique

    2016-10-24

    The aromatic osmacyclopropenefuran bicycles [OsTp{κ(3) -C(1) ,C(2) ,O-(C(1) H2 C(2) CHC(OEt)O)}(P(i) Pr3 )]BF4 (Tp=hydridotris(1-pyrazolyl)borate) and [OsH{κ(3) -C(1) ,C(2) ,O-(C(1) H2 C(2) CHC(OEt)O)}(CO)(P(i) Pr3 )2 ]BF4 , with the metal fragment in a common vertex between the fused three- and five-membered rings, have been prepared via the π-allene intermediates [OsTp(η(2) -CH2 =CCHCO2 Et)(OCMe2 )(P(i) Pr3 )]BF4 and [OsH(η(2) -CH2 =CCHCO2 Et)(CO)(OH2 )(P(i) Pr3 )2 ]BF4 , and their aromaticity analyzed by DFT calculations. The bicycle containing the [OsH(CO)(P(i) Pr3 )2 ](+) metal fragment is a key intermediate in the [OsH(CO)(OH2 )2 (P(i) Pr3 )2 ]BF4 -catalyzed regioselective anti-Markovnikov hydration of ethyl buta-2,3-dienoate to ethyl 4-hydroxycrotonate.

  7. Statistical Features of EMIC Waves Observed on Van Allen Probes in the Inner Magnetosphere

    NASA Astrophysics Data System (ADS)

    Lee, D. Y.; Roh, S. J.; Cho, J.; Shin, D. K.; Hwang, J.; Kim, K. C.; Kurth, W. S.; Kletzing, C.; Wygant, J. R.; Thaller, S. A.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves are one of the key plasma waves that can affect charged particle dynamics in the Earth's inner magnetosphere. Knowledge of global distribution of the EMIC waves is critical for accurately assessing the significance of its interaction with charged particles. With the Van Allen Probes EMFISIS observations, we have surveyed EMIC events for ~2.5 years period. We have identified well-defined, banded wave activities only, as distinguished from broad band wave activities. We have obtained global distribution of occurrence of the identified waves with distinction between H- and He-bands. We compare it with previous observations such as THEMIS and CRRES. For the identified events we have drawn all the basic wave properties including wave frequency, polarization, wave normal angle. In addition, we have distinguished the EMIC events that occur inside the plasmasphere and at the plasmapause from those outside the plasmasphere. Finally, we have tested solar wind and geomagnetic dependence of the wave events. We give discussions about implications of these observations on wave generation mechanism and interaction with radiation belt electrons.

  8. Variation of energetic electron flux in Earth's radiation belts based on Van Allen Probes observations

    NASA Astrophysics Data System (ADS)

    Tang, Rongxin; Zhong, Zhihong; Yu, Deyin

    2016-04-01

    The Earth's radiation belts have been an important research topic of solar-terrestrial physics from 1958. In 2012, Van Allen Probes (VAP) were launched into near-equatorial orbit and provide very good in-situ observations of energetic particles in inner magnetosphere. Since magnetospheric substorm can cause the severe disturbance of the Earth's megnetospheric environment, here we focus on the characteristics of energetic electron fluxes in the radiation belts during substorm time and non-storm time. Energetic electron data observed by the Magnetic Electron Ion Spectrometer (MagEIS) and Energetic Particle Composition and Thermal Plasma Suite (ECT) of VAP during 2012 to 2014 are carefully analyzed. We select portions of energetic electron data from substorm onset phase, growth phase, recovery phase, and quiet time, and make a comparisons with theoretical computations. We find that the electron differential fluxes present E-1 shape at lower energies (<1MeV), and have a sharp transition with steeper slopes at high energies for large L-shells, which are in coincidence with Mauk's model [Mauk et al., 2010].

  9. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    DOE PAGES

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; ...

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5more » to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.« less

  10. Study of lightning whistler waves observed at high L-shells on Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Holzworth, R.; Brundell, J. B.; Wygant, J. R.; Hospodarsky, G. B.; Mozer, F.; Jacobson, A. R.; Bonnell, J. W.

    2015-12-01

    Lightning produces strong broadband radio waves, called "sferics", which propagate in the Earth-ionosphere waveguide and are detected thousands of kilometers away from their source. Global real-time detection of lightning strokes including their time, location and energy, is conducted with the World Wide Lightning Location Network (WWLLN). In the ionosphere, these sferics couple into very low frequency (VLF) whistler waves which propagate obliquely to the Earth's magnetic field. In our previous work, one-to-one coincidence between lightning and whistler waves is already found by the conjunction work between WWLLN and Van Allen Probes (formerly known as the Radiation Belt Storm Probes (RBSP)). The previous global study showed a good match between WWLLN sferics and RBSP lightning whistlers at low L-shell region (L < 3). More case studies indicated that this kind of one-to-one coincidence can be extended to a high L-shell region. Since September 2012 to now (July 2015), EMFISIS instrument has already recorded 3-D waveform data with 35 ksamples/s for 527,279 and 542,346 of 6-second snapshots, respectively for RBSP-A and RBSP-B. 461,572 and 478,510 of snapshots with L-shell value larger than 3 are used in our work. In our work, we will show the distribution of lightning whistler waves at high L-shells. This talk will also explore the upper cutoff frequency of lightning whistler waves at high L-shells.

  11. "Trunk-like" heavy ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.-C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. We report "trunk-like" ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L = 3.6-2.6, magnetic local time (MLT) = 9.1-10.5, and magnetic latitude (MLAT) = -2.4-0.09°, vary monotonically from 3.5 to 0.04 keV. The values at the two end points of the O+ trunk are energy = 4.5-0.7 keV, L = 3.6-2.5, MLT = 9.1-10.7, and MLAT = -2.4-0.4°. Results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  12. A background correction algorithm for Van Allen Probes MagEIS electron flux measurements

    SciTech Connect

    Claudepierre, S. G.; O'Brien, T. P.; Blake, J. B.; Fennell, J. F.; Roeder, J. L.; Clemmons, J. H.; Looper, M. D.; Mazur, J. E.; Mulligan, T. M.; Spence, H. E.; Reeves, G. D.; Friedel, R. H. W.; Henderson, M. G.; Larsen, B. A.

    2015-07-14

    We describe an automated computer algorithm designed to remove background contamination from the Van Allen Probes Magnetic Electron Ion Spectrometer (MagEIS) electron flux measurements. We provide a detailed description of the algorithm with illustrative examples from on-orbit data. We find two primary sources of background contamination in the MagEIS electron data: inner zone protons and bremsstrahlung X-rays generated by energetic electrons interacting with the spacecraft material. Bremsstrahlung X-rays primarily produce contamination in the lower energy MagEIS electron channels (~30–500 keV) and in regions of geospace where multi-M eV electrons are present. Inner zone protons produce contamination in all MagEIS energy channels at roughly L < 2.5. The background-corrected MagEIS electron data produce a more accurate measurement of the electron radiation belts, as most earlier measurements suffer from unquantifiable and uncorrectable contamination in this harsh region of the near-Earth space environment. These background-corrected data will also be useful for spacecraft engineering purposes, providing ground truth for the near-Earth electron environment and informing the next generation of spacecraft design models (e.g., AE9).

  13. Explaining the dynamics of the ultra-relativistic third Van Allen radiation belt

    DOE PAGES

    Mann, I. R.; Ozeke, L. G.; Murphy, K. R.; ...

    2016-06-20

    Since the discovery of the Van Allen radiation belts over 50 years ago, an explanation for their complete dynamics has remained elusive. Especially challenging is understanding the recently discovered ultra-relativistic third electron radiation belt. Current theory asserts that loss in the heart of the outer belt, essential to the formation of the third belt, must be controlled by high-frequency plasma wave–particle scattering into the atmosphere, via whistler mode chorus, plasmaspheric hiss, or electromagnetic ion cyclotron waves. However, this has failed to accurately reproduce the third belt. In this paper, using a data-driven, time-dependent specification of ultra-low-frequency (ULF) waves we showmore » for the first time how the third radiation belt is established as a simple, elegant consequence of storm-time extremely fast outward ULF wave transport. High-frequency wave–particle scattering loss into the atmosphere is not needed in this case. Finally, when rapid ULF wave transport coupled to a dynamic boundary is accurately specified, the sensitive dynamics controlling the enigmatic ultra-relativistic third radiation belt are naturally explained.« less

  14. Explaining the dynamics of the ultra-relativistic third Van Allen radiation belt

    SciTech Connect

    Mann, I. R.; Ozeke, L. G.; Murphy, K. R.; Claudepierre, S. G.; Turner, D. L.; Baker, D. N.; Rae, I. J.; Kale, A.; Milling, D. K.; Boyd, A. J.; Spence, H. E.; Reeves, Geoffrey D.; Singer, H. J.; Dimitrakoudis, S.; Daglis, I. A.; Honary, F.

    2016-06-20

    Since the discovery of the Van Allen radiation belts over 50 years ago, an explanation for their complete dynamics has remained elusive. Especially challenging is understanding the recently discovered ultra-relativistic third electron radiation belt. Current theory asserts that loss in the heart of the outer belt, essential to the formation of the third belt, must be controlled by high-frequency plasma wave–particle scattering into the atmosphere, via whistler mode chorus, plasmaspheric hiss, or electromagnetic ion cyclotron waves. However, this has failed to accurately reproduce the third belt. In this paper, using a data-driven, time-dependent specification of ultra-low-frequency (ULF) waves we show for the first time how the third radiation belt is established as a simple, elegant consequence of storm-time extremely fast outward ULF wave transport. High-frequency wave–particle scattering loss into the atmosphere is not needed in this case. Finally, when rapid ULF wave transport coupled to a dynamic boundary is accurately specified, the sensitive dynamics controlling the enigmatic ultra-relativistic third radiation belt are naturally explained.

  15. A background correction algorithm for Van Allen Probes MagEIS electron flux measurements

    DOE PAGES

    Claudepierre, S. G.; O'Brien, T. P.; Blake, J. B.; ...

    2015-07-14

    We describe an automated computer algorithm designed to remove background contamination from the Van Allen Probes Magnetic Electron Ion Spectrometer (MagEIS) electron flux measurements. We provide a detailed description of the algorithm with illustrative examples from on-orbit data. We find two primary sources of background contamination in the MagEIS electron data: inner zone protons and bremsstrahlung X-rays generated by energetic electrons interacting with the spacecraft material. Bremsstrahlung X-rays primarily produce contamination in the lower energy MagEIS electron channels (~30–500 keV) and in regions of geospace where multi-M eV electrons are present. Inner zone protons produce contamination in all MagEIS energymore » channels at roughly L < 2.5. The background-corrected MagEIS electron data produce a more accurate measurement of the electron radiation belts, as most earlier measurements suffer from unquantifiable and uncorrectable contamination in this harsh region of the near-Earth space environment. These background-corrected data will also be useful for spacecraft engineering purposes, providing ground truth for the near-Earth electron environment and informing the next generation of spacecraft design models (e.g., AE9).« less

  16. Can You Hear Me Now? Software Development at the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Castellanos, Aaron; Harp, G.

    2013-01-01

    The Allen Telescope Array (ATA) is a 42 radio dish array located in Hat Creek, CA and is used to search for traces of Extraterrestrial Intelligence (SETI) and to study the interstellar medium. In order to minimize the Radio Frequency Interference (RFI) that leaks into the antennas of the ATA and gain a stronger signal along with a clearer picture of the sky, we must analyze the array to determine which antennas are operating best. Readgains is a new tool that we developed to generate the system temperatures of the dishes and if they are below a given threshold (e.g. 150 K), we use them for observations. We conducted a five week observation of the galaxy 3c286 in order to study the behavior of the array and concluded that most operating antennas are performing well and the ones that were not will be excluded in the next observations. Hat Creek Radio Observatory will continue to use this tool for continuous analysis of the array.

  17. Pulsating aurora observed on the ground and in-situ by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Lessard, M.; Cohen, I. J.; Denton, R. E.; Engebretson, M. J.; Kletzing, C.; Wygant, J. R.; Bounds, S. R.; Smith, C. W.; MacDowall, R. J.; Kurth, W. S.

    2013-12-01

    Early observations and theory related to pulsating aurora suggested that the electrons that drive this aurora originate from the equatorial region of the magnetosphere and that a likely process that can scatter these electrons would involve chorus waves. Recent satellite observations during pulsating auroral events have provided important "firsts", including evidence of strong correlations between pulsating auroral patches and in-situ lower-band chorus (THEMIS), as well as correlations with energetic electron precipitation in the vicinity of geosynchronous orbit (GOES). These results provide important information regarding particle dynamics, leading to a question about how the chorus might be driven. We present observations of the Van Allen Probes in conjunction with a pulsating aurora event, as confirmed by observations on the ground. The in-situ data again show the presence of lower-band chorus. However, magnetic and electric field data also show that the wave bursts coincide with an apparent poloidal field-line resonance, begging the question of whether the resonance might be responsible for driving the VLF waves.

  18. ACE EPAM and Van Allen Probes RBSPICE measurements of interplanetary oxygen injection to the inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Patterson, J. D.; Manweiler, J. W.; Gerrard, A. J.; Lanzerotti, L. J.

    2015-12-01

    On March 17, 2015, a significant oxygen-rich interplanetary event was measure by the Advanced Composition Explorer (ACE) Electron Proton Alpha Monitor (EPAM) instrument. At the same time the Van Allen Probes Radiation Belt Storm Probes Ion Composition Experiment (RBSPICE) instrument recorded significant enhancements of oxygen in the inner magnetosphere. We present a detailed analysis of this event utilizing a new method of exploiting the EPAM Pulse Height Analyzer (PHA) data to precisely resolve helium and oxygen spectra within the 0.5 to 5 MeV/nuc range. We also present the flux, partial particle pressures, and pitch angle distributions of the ion measurements from RBSPICE. During this event, both EPAM and RBSPICE measured O:He ratios greater than 10:1. The pitch angle distributions from RBSPICE-B show a strong beam of oxygen at an L ~ 5.8 early on March 17th during orbit. The timing between the observations of the oxygen peak at ACE and the beam observed at RBSPICE-B is consistent with the travel-time required for energetic particle transport from L1 to Earth and access to the magnetosphere. We assert that the oxygen seen by RBSPICE during the initial phase of this event is the result of direct injection from the interplanetary medium of energetic ions. This poster contains the observations and detailed calculations to support this assertion.

  19. Improved lattice Boltzmann modeling of binary flow based on the conservative Allen-Cahn equation

    NASA Astrophysics Data System (ADS)

    Ren, Feng; Song, Baowei; Sukop, Michael C.; Hu, Haibao

    2016-08-01

    The primary and key task of binary fluid flow modeling is to track the interface with good accuracy, which is usually challenging due to the sharp-interface limit and numerical dispersion. This article concentrates on further development of the conservative Allen-Cahn equation (ACE) [Geier et al., Phys. Rev. E 91, 063309 (2015), 10.1103/PhysRevE.91.063309] under the framework of the lattice Boltzmann method (LBM), with incorporation of the incompressible hydrodynamic equations [Liang et al., Phys. Rev. E 89, 053320 (2014), 10.1103/PhysRevE.89.053320]. Utilizing a modified equilibrium distribution function and an additional source term, this model is capable of correctly recovering the conservative ACE through the Chapman-Enskog analysis. We also simulate four phase-tracking benchmark cases, including one three-dimensional case; all show good accuracy as well as low numerical dispersion. By coupling the incompressible hydrodynamic equations, we also simulate layered Poiseuille flow and the Rayleigh-Taylor instability, illustrating satisfying performance in dealing with complex flow problems, e.g., high viscosity ratio, high density ratio, and high Reynolds number situations. The present work provides a reliable and efficient solution for binary flow modeling.

  20. A long-lived relativistic electron storage ring embedded in Earth's Outer Van Allen belt

    DOE PAGES

    Baker, D. N.; Kanekal, S. G.; Hoxie, V. C.; ...

    2013-02-28

    Since their discovery over 50 years ago, the Earth’s Van Allen radiation belts are thought to consist of two distinct zones of trapped, highly energetic charged particles. The outer zone is comprised predominantly of mega-electron volt (MeV) electrons that wax and wane in intensity on time scales ranging from hours to days depending primarily on external forcing by the solar wind. Thus, the spatially separated inner zone is comprised of commingled high-energy electrons and very energetic positive ions (mostly protons), the latter being stable in intensity levels over years to decades. In situ energy-specific and temporally resolved spacecraft observations revealmore » an isolated third ring, or torus, of high-energy (E > 2 MeV) electrons that formed on 2 September 2012 and persisted largely unchanged in the geocentric radial range of 3.0 to ~3.5 Earth radii for over four weeks before being disrupted (and virtually annihilated) by a powerful interplanetary shock wave passage.« less

  1. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    SciTech Connect

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5 to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  2. Cellular localization and detergent dependent oligomerization of rice allene oxide synthase-1.

    PubMed

    Yoeun, Sereyvath; Kim, Jeong-Il; Han, Oksoo

    2015-01-01

    Allene oxide synthase-1 from Oryza sativa (OsAOS1) localizes to the chloroplast, but lacks a putative chloroplast targeting sequence typically found in dicot AOS. Here, kinetic parameters and the oligomerization state/subunit composition of OsAOS1 were characterized in vitro in the absence or presence of detergent micelles. The catalytic efficiency (k(cat)/K(m)) of OsAOS1 reached a maximum near the critical micelle concentration for polyoxyethylene 10 tridecyl ether. Native gel analysis showed that OsAOS1 exists as a multimer in the absence of detergent micelles. The multimeric form of OsAOS1 was stably cross-linked in the absence of detergents, while only monomeric OsAOS1 was detected in the presence of detergent micelles. Gel filtration analysis indicated that the oligomeric state of OsAOS1 depends strongly on the detergents and that the monomer becomes the predominant form in the presence of detergent micelles. These data suggest that the detergent-dependent oligomeric state of OsAOS1 is an important factor for the regulation of its catalytic efficiency.

  3. New chorus wave properties near the equator from Van Allen Probes wave observations

    NASA Astrophysics Data System (ADS)

    Li, W.; Santolik, O.; Bortnik, J.; Thorne, R. M.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.

    2016-05-01

    The chorus wave properties are evaluated using Van Allen Probes data in the Earth's equatorial magnetosphere. Two distinct modes of lower band chorus are identified: a quasi-parallel mode and a quasi-electrostatic mode, whose wave normal direction is close to the resonance cone. Statistical results indicate that the quasi-electrostatic (quasi-parallel) mode preferentially occurs during relatively quiet (disturbed) geomagnetic activity at lower (higher) L shells. Although the magnetic intensity of the quasi-electrostatic mode is considerably weaker than the quasi-parallel mode, their electric intensities are comparable. A newly identified feature of the quasi-electrostatic mode is that its frequency peaks at higher values compared to the quasi-parallel mode that exhibits a broad frequency spectrum. Moreover, upper band chorus wave normal directions vary between 0° and the resonance cone and become more parallel as geomagnetic activity increases. Our new findings suggest that chorus-driven energetic electron dynamics needs a careful examination by considering the properties of these two distinct modes.

  4. Thermal conversions of fatty acid peroxides to cyclopentenones: a biomimetic model for allene oxide synthase pathway.

    PubMed

    Mukhtarova, Lucia S; Mukhitova, Fakhima K; Grechkin, Alexander N

    2013-01-01

    The trimethylsilyl (TMS) peroxides of linoleic acid 9(S)-hydroperoxide (TMS or Me esters) were subjected to gas chromatography-mass spectrometry (GC-MS) analyses. The cyclopentenones, trans- and cis-10-oxo-11-phytoenoic acid (10-oxo-PEA, Me or TMS esters) were first time detected as the products of TMS-peroxide thermal conversions. The major products were ketodienes, epoxyalcohols, hemiacetals and decadienals. For further study of thermal cyclopentenone formation, 9(S)- or 13(S)-hydroperoxides of linoleic acid (Me esters) were sealed in ampoules and heated at 230 °C for 15 or 30 min. The products were separated by HPLC. The cyclopentenone fractions were collected and analyzed by GC-MS. Trans-10-oxo-PEA (Me) and 10-oxo-9(13)-PEA (Me) were formed during the thermal conversion of 9-hydroperoxide (Me ester). Similarly, the cyclopentenones trans-12-oxo-PEA (Me) and 12-oxo-9(13)-PEA (Me) were detected after the heating of 13-hydroperoxide (Me ester). Thermal formation of cyclopentenones can be considered as a biomimetic model of AOS pathway, providing new insights into the mechanisms of allene oxide formation and cyclization.

  5. A long-lived relativistic electron storage ring embedded in Earth's Outer Van Allen belt

    SciTech Connect

    Baker, D. N.; Kanekal, S. G.; Hoxie, V. C.; Henderson, M. G.; Li, X.; Spence, H. E.; Elkington, S. R.; Friedel, R. H. W.; Goldstein, J.; Hudson, M. K.; Reeves, G. D.; Thorne, R. M.; Kletzing, C. A.; Claudepierre, S. G.

    2013-02-28

    Since their discovery over 50 years ago, the Earth’s Van Allen radiation belts are thought to consist of two distinct zones of trapped, highly energetic charged particles. The outer zone is comprised predominantly of mega-electron volt (MeV) electrons that wax and wane in intensity on time scales ranging from hours to days depending primarily on external forcing by the solar wind. Thus, the spatially separated inner zone is comprised of commingled high-energy electrons and very energetic positive ions (mostly protons), the latter being stable in intensity levels over years to decades. In situ energy-specific and temporally resolved spacecraft observations reveal an isolated third ring, or torus, of high-energy (E > 2 MeV) electrons that formed on 2 September 2012 and persisted largely unchanged in the geocentric radial range of 3.0 to ~3.5 Earth radii for over four weeks before being disrupted (and virtually annihilated) by a powerful interplanetary shock wave passage.

  6. "Zipper-like" periodic magnetosonic waves: Van Allen Probes, THEMIS, and magnetospheric multiscale observations

    NASA Astrophysics Data System (ADS)

    Li, J.; Bortnik, J.; Li, W.; Ma, Q.; Thorne, R. M.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.; Wygant, J.; Breneman, A.; Thaller, S.; Funsten, H. O.; Mitchell, D. G.; Manweiler, J. W.; Torbert, R. B.; Le Contel, O.; Ergun, R. E.; Lindqvist, P.-A.; Torkar, K.; Nakamura, R.; Andriopoulou, M.; Russell, C. T.

    2017-02-01

    An interesting form of "zipper-like" magnetosonic waves consisting of two bands of interleaved periodic rising-tone spectra was newly observed by the Van Allen Probes, the Time History of Events and Macroscale Interactions during Substorms (THEMIS), and the Magnetospheric Multiscale (MMS) missions. The two discrete bands are distinct in frequency and intensity; however, they maintain the same periodicity which varies in space and time, suggesting that they possibly originate from one single source intrinsically. In one event, the zipper-like magnetosonic waves exhibit the same periodicity as a constant-frequency magnetosonic wave and an electrostatic emission, but the modulation comes from neither density fluctuations nor ULF waves. A statistical survey based on 3.5 years of multisatellite observations shows that zipper-like magnetosonic waves mainly occur on the dawnside to noonside, in a frequency range between 10 fcp and fLHR. The zipper-like magnetosonic waves may provide a new clue to nonlinear excitation or modulation process, while its cause still remains to be fully understood.

  7. A Neural Network Approach for Identifying Relativistic Electron Pitch Angle Distributions in Van Allen Probes Data

    NASA Astrophysics Data System (ADS)

    Souza, V. M. C. E. S.; Vieira, L.; Alves, L. R.; Da Silva, L. A.; Koga, D.; Sibeck, D. G.; Walsh, B.; Kanekal, S. G.; Silveira, M. D.; Medeiros, C.; Mendes, O., Jr.; Marchezi, J.; Rockenbach, M.; Jauer, P. R.; Gonzalez, W.; Baker, D. N.

    2015-12-01

    A myriad of physical phenomena occur in the inner magnetosphere, in particular at the Earth's radiation belts, which can be a result of the combination of both internal and external processes. However, the connection between physical processes occurring deep within the magnetosphere and external interplanetary drivers it is not yet well understood. In this work we investigate whether a selected set of interplanetary structures affect the local time distribution of three different classes of high energy electron pitch angle distributions (PADs), namely normal, isotropic, and butterfly. We split this work into two parts: initially we focus on the methodology used which employs a Self-Organized Feature Map (SOFM) neural network for identifying different classes of electron PAD shapes in the Van Allen Probes' Relativistic Electron Proton Telescope (REPT) data. The algorithm can categorize the input data into an arbitrary number of classes from which three of them appears the most: normal, isotropic and butterfly. Other classes which are related with these three also emerge and deserve to be addressed in detail in future works. We also discuss the uncertainties of the algorithm. Then, we move to the second part where we describe in details the criteria used for selecting the interplanetary events, and also try to investigate the relation between key parameters characterizing such interplanetary structures and the local time distributions of electron PAD shapes.

  8. Explaining the dynamics of the ultra-relativistic third Van Allen radiation belt

    NASA Astrophysics Data System (ADS)

    Mann, I. R.; Ozeke, L. G.; Murphy, K. R.; Claudepierre, S. G.; Turner, D. L.; Baker, D. N.; Rae, I. J.; Kale, A.; Milling, D. K.; Boyd, A. J.; Spence, H. E.; Reeves, G. D.; Singer, H. J.; Dimitrakoudis, S.; Daglis, I. A.; Honary, F.

    2016-10-01

    Since the discovery of the Van Allen radiation belts over 50 years ago, an explanation for their complete dynamics has remained elusive. Especially challenging is understanding the recently discovered ultra-relativistic third electron radiation belt. Current theory asserts that loss in the heart of the outer belt, essential to the formation of the third belt, must be controlled by high-frequency plasma wave-particle scattering into the atmosphere, via whistler mode chorus, plasmaspheric hiss, or electromagnetic ion cyclotron waves. However, this has failed to accurately reproduce the third belt. Using a data-driven, time-dependent specification of ultra-low-frequency (ULF) waves we show for the first time how the third radiation belt is established as a simple, elegant consequence of storm-time extremely fast outward ULF wave transport. High-frequency wave-particle scattering loss into the atmosphere is not needed in this case. When rapid ULF wave transport coupled to a dynamic boundary is accurately specified, the sensitive dynamics controlling the enigmatic ultra-relativistic third radiation belt are naturally explained.

  9. Low Energy Plasma Measurements of the Van Allen Probes Crossing Open Field Lines

    NASA Astrophysics Data System (ADS)

    Larsen, B.; MacDonald, E.; Skoug, R. M.; Dixon, P.; Henderson, M. G.; Chaston, C. C.; Grande, M.; Funsten, H. O.; Thomsen, M.; Wygant, J. R.; Reeves, G. D.

    2013-12-01

    The Van Allen Probes encountered unusual low-latitude flank-side open field lines during the Nov. 14 2012 geomagnetic storm. Both spacecraft entered the lobes five times over several hours in the main phase of the storm. Four of the ~ five minute events were seen by both probes nearly simultaneously despite being 45 minutes apart in orbit (less than one L shell). The more tailward satellite always saw the boundary crossing first. We present the HOPE low energy plasma observations during these encounters. Adjacent to the lobe intervals, HOPE observed a hot electron plasma sheet leading to significant spacecraft charging. The electron and ion fluxes were significantly diminished during the lobe crossings coincident with a stronger, more highly stretched magnetic field. Significant accelerated field aligned oxygen signatures were measured on both closed and apparently open field lines, along with strong Alfvenic waves. Using the multipoint measurements we will examine the source of this acceleration and its role in inner magnetosphere ion dynamics. This event also represents the chance to constrain and assess magnetic field models and we will examine the topological location of the field lobes relative to the spacecraft for multiple models.

  10. Correlations between chorus properties and electron velocity distributions: Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Fu, X.; Cowee, M.; Gary, S. P.; Liu, K.; Min, K.; Winske, D.

    2014-12-01

    Magnetospheric chorus consists of whistler waves driven unstable by anisotropicelectron velocity distributions. A gap in the power spectrum of chorus at a fre-quency close to half the electron cyclotron frequency (Ωe/2) are often observedso that chorus can be categorized into four types accordingly: banded chorus(with two bands in the spectrum separated by Ωe/2), lower band only (withonly one band below Ωe/2), upper band only (with only one band above Ωe/2)and broadband (with only one band including Ωe/2). Here we present a studyto correlate chorus properties with electron velocity distributions based on thehypothesis that each band of chorus is excited by an anisotropic electron com-ponent. On Jan 14 2013, Van Allen Probes satellite A measured strong chorusactivity, and all four types were observed. We analyze HOPE and EMFISIS dataand show that there is a good correlation between the observed wave frequencyand propagation direction and the predictions of kinetic linear dispersion theoryusing electron component densities and temperatures obtained by fitting HOPEdata to a multi-component bi-Maxwellian distribution function. However, thetemperature anisotropies observed by HOPE are usually close to the instabil-ity threshold and therefore it is not possible at this point to predict whether acertain band can be excited based on measured electron velocity distributions.LA-UR-14-26177.

  11. A GENERATIVE MODEL FOR MULTI-ATLAS SEGMENTATION ACROSS MODALITIES

    PubMed Central

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Van Leemput, Koen

    2013-01-01

    Current label fusion methods enhance multi-atlas segmentation by locally weighting the contribution of the atlases according to their similarity to the target volume after registration. However, these methods cannot handle voxel intensity inconsistencies between the atlases and the target image, which limits their application across modalities or even across MRI datasets due to differences in image contrast. Here we present a generative model for multi-atlas image segmentation, which does not rely on the intensity of the training images. Instead, we exploit the consistency of voxel intensities within regions in the target volume and their relation to the propagated labels. This is formulated in a probabilistic framework, where the most likely segmentation is o